CN111445768B - Modular assembly peptide chain space structure model - Google Patents
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Abstract
The invention provides a modular assembly peptide chain space structure model which comprises a plurality of first basic modules and a plurality of second basic modules. The invention can directly show the relationship of each atom and each adjacent chemical bond of the peptide plane, can resist repeated rotation without loosening, has stable conformation, and can directly measure or visually obtain the angle value by manufacturing the peptide plane into a plane structure to replace the traditional ball stick model, enabling the imino end and the carbonyl end to be detachable, manufacturing the linking point C alpha of the adjacent peptide plane into a ball model as a connecting pivot, and using a sleeve pipe for connecting to replace the ball stick. The invention builds a reality model for any teacher according to theoretical data, simplifies, realizes three-dimensional, actualized and vivid teaching, facilitates the teaching of the teacher, and simultaneously improves the learning interest of students and deepens the understanding and mastering of difficult knowledge.
Description
Technical Field
The invention relates to a modular assembly peptide chain space structure model, and belongs to the technical field of teaching and scientific research tools.
Background
Proteins, which are commonly present in the biological world, are the most important biological macromolecules in the body of an organism, are the basic material basis for life activities, and perform different physiological functions respectively. Through the research of the structure and the function correlation of a large number of proteins, the proteins with different biological functions are found to contain different spatial structures; the specific spatial conformation of the protein in vivo is closely related to the physiological function of the protein. Therefore, studying the structure of a protein is critical to studying its function.
Protein molecules are biological macromolecules formed by many amino acids connected by peptide bonds and play important biological functions in the life activities of organisms. The specific spatial structure of a protein is the structural basis for its function, and therefore, it is important to study the structure of a protein to study its function. The molecular structure of protein is divided into four grades, i.e. primary, secondary, tertiary and quaternary structure, the sequence of amino acids composing protein is the primary structure of protein, the latter three are called as the high-level structure or space conformation of protein. The basic building block of proteins is an amino acid. Peptide bonds are the basic means of amino acid attachment, and are partially double-bonded in nature and are not free to rotate due to resonant interactions between the amide nitrogen and the carboxyl oxygen, and therefore the six atoms C α 1, C, O, N, H, C α 2 involved in the formation of peptide bonds are in one plane, referred to as the peptide plane (or amide plane). The peptide plane (amide plane) is the basic structural unit of the spatial structure of proteins. The conventional ball stick model shows a single peptide plane, and the peptide plane is not really designed on the same plane entity by the imagination of people, so that students are difficult to really understand and master in teaching, and teachers are difficult to thoroughly explain the key content. And the prior patent technology: a modular assembly protein structure model (CN 201510262260.0) discloses a ball stick structure of peptide planes and a method for assembling protein space structure, which is formed to lack the sense of flatness, so that the difficult understanding points related to the peptide planes, such as phi angle and psi angle, are more abstract and lack intuitiveness.
The peptide plane (amide plane) is the basic structural unit of the spatial structure of proteins. The secondary structure of protein is relative space position of backbone atom of protein backbone, and is local space structure of a certain peptide segment of protein molecule, including alpha helix, beta sheet, beta turn and random coil. Alpha helix, beta sheet, is the most common basic structural model for protein secondary structure.
Pauling and Corey suggested that alpha helices (α -helix) and β sheets (β -pleated sheet) are the major forms of protein secondary structure based on experimental data. In the alpha helix (alpha-helix) structure, the polypeptide chain backbone rises spirally about a central axis, the helix runs in a clockwise right-handed helix with a phi angle of-47 deg., a psi angle of-57 deg., and the side chain R groups of the amino acid extend outside the helix, depending on the direction of the peptide chain from the amino terminus (N-terminus) to the carboxy terminus (C-terminus). Each 3.6 amino acid residue was spiraled up one turn (i.e., rotated 360 °) at a pitch of 0.54 nm. The N-H of each peptide bond of the alpha helix and the carbonyl oxygen of the fourth peptide bond form a hydrogen bond, the direction of which is substantially parallel to the long axis of the helix. All of the carbonyl oxygens in all peptide bonds in the peptide chain can form hydrogen bonds to stabilize the alpha helical structure. Beta-sheet is folded, polypeptide chains are fully extended, each peptide plane (peptide unit) takes C alpha as a rotation point, the peptide plane is folded in sequence to form a saw-toothed structure, amino acid residue side chains are alternately positioned above and below the saw-toothed structure, the saw-toothed structures of a plurality of peptide segments in one peptide chain can be arranged in parallel, two peptide segments which are far away from each other in a molecule can form the same trend through folding, and can also form the opposite trend through folding.
When the teacher teaches the secondary structure of the protein, the teacher only depends on the textbook graph and the simple two-dimensional graph to help the students to understand and master, so that the students are difficult to understand intuitively. In the existing process of teaching and scientific research on protein structural functions, a basic model which can simply and visually display the spatial structure of a peptide chain is not available. And the prior patent technology: a modular assembly protein structure model (CN 201510262260.0) device is difficult to actually lay out and simulate a real protein space structure. Based on the structure characteristics of amino acids, peptide plane characteristics and secondary structure model characteristics of the constituent proteins, the invention designs a model which can truly simulate a peptide plane and can be assembled into a protein secondary structure, in particular to a model of a basic structure of an alpha helix and a beta folding alpha turn, and provides a model basis for the teaching and scientific research of protein structure science.
Disclosure of Invention
The invention provides a modular assembly peptide chain space structure model based on theoretical data support of protein structure, overcomes the defects of lack of intuition and operability in the prior art, and is used for teaching and scientific research of protein structures and building a realistic model for teachers and scientific researchers. The teaching is simplified, three-dimensional, realistic and vivid, the teaching of teachers is facilitated, the learning interest of students is improved, and the understanding and mastering of difficult knowledge are deepened.
In order to achieve the purpose, the invention adopts the following technical means:
the invention provides a modular assembly peptide chain space structure model, which is characterized by comprising a plurality of first basic modules and a plurality of second basic modules, wherein:
the main body of the first basic module is a plate, the position of the center of the plate, which is towards the left, is provided with a C atom mark, the position of the center of the plate, which is towards the right, is provided with an N atom mark, the position of the upper left corner of the plate is provided with an O atom mark, and the position of the lower right corner of the plate is provided with an H atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark is arranged between the N atom mark and the H atom mark, a single bond mark and a triangular mark for indicating a rotation angle measuring position are arranged at the left lower corner of the C atom mark and the plate, and a single bond mark and a triangular mark for indicating a rotation angle measuring position are arranged at the right upper corner of the N atom mark and the plate; a first imaginary line segment is arranged at the center of the C atom mark and the center of the N atom mark, a second imaginary line segment is arranged at the center of the C atom mark and the center of the O atom mark, a third imaginary line segment is arranged at the center of the N atom mark and the center of the H atom mark, a fourth imaginary line segment is arranged at the center of the C atom mark and the lower left corner of the plate, and a fifth imaginary line segment is arranged at the center of the N atom mark and the upper right corner of the plate; the plate is provided with two through holes on two imaginary straight lines of the fourth imaginary line segment and the fifth imaginary line segment and can be inserted into the second basic module;
the main body of the second basic module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with a-NH mark which can be inserted into the right upper corner hole of the first basic module, the long pipe with the thin disc in the rear is provided with a-CO mark which can be inserted into the left lower corner hole of the first basic module, and the long pipe without the thin disc is provided with a-R mark.
Preferably, in the first basic block, the length of the first virtual line segment is 5.28 length units, the length of the second virtual line segment is 4.92 length units, the length of the third virtual line segment is 4.04 length units, the length of the fourth virtual line segment is 6.12 length units, the length of the fifth virtual line segment is 5.88 length units, and the inner diameters of the two through holes are 1.6 length units; an included angle between the first imaginary line segment and the second imaginary line segment is 123.5 °, an included angle between the first imaginary line segment and the third imaginary line segment is 120 °, an included angle between the first imaginary line segment and the fourth imaginary line segment is 116 °, and an included angle between the first imaginary line segment and the fifth imaginary line segment is 122 °; the first base module is shown in an unmarked top view in fig. 3, a marked top view in fig. 4 and a front view in fig. 5;
in the second basic module, the outer diameters of four tubes are all 1.6 length units, the included angle between the long tube with the-NH map and the long tube with the-CO map is 111 degrees, the included angle between the long tube with the-R map and the long tube with the-NH map is 110.6 degrees, the included angle between the long tube with the-R map and the long tube with the-CO map is 110.6 degrees, the included angles between the short tube connecting the sphere and the three long tubes are 108.2 degrees respectively, the lengths of the three long tubes are 5.6 length units, the long tube with the-R mark is provided with an annular mark at a position 2.24-2.36 length units away from the center of the module, the length of one short tube is 5 length units, the diameter of the sphere is 2.96 length units, and the two thin disks are 3.5 length units away from the center of the module, and a protractor with 360-degree scales is pasted outside, and the 0-degree line of the protractor is positioned on a plane formed by the intersection of the central lines of the two long pipes; the second base module is shown in top plan view and front view in fig. 6 and 7.
Preferably, the model further comprises a plurality of third basic modules and a plurality of fourth basic modules, wherein:
the third basic module and the fourth basic module are respectively a left half block and a right half block of the first basic module, and splicing structures which can be spliced with each other are arranged at the splitting positions; top views of the third and fourth base modules are shown in fig. 8 and 9.
Preferably, the model further comprises a plurality of first special modules, a plurality of second special modules and a plurality of third special modules, wherein:
the main body of the first special module is a plate, the position of the center of the plate, which is towards the left, is provided with a C atom mark, the position of the center of the plate, which is towards the right, is provided with an N atom mark, and the position of the upper left corner of the plate is provided with an O atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark and a triangular mark for indicating a rotation angle measuring position are arranged at the left lower corner position of the C atom mark and the plate, a single bond mark and a triangular mark for indicating a rotation angle measuring position are arranged at the right upper corner position of the N atom mark and the plate, and a single bond mark is arranged between the N atom mark and the right lower corner position of the plate; a first imaginary line segment is arranged at the center of the C atom mark and the center of the N atom mark, a second imaginary line segment is arranged at the center of the C atom mark and the center of the O atom mark, a third imaginary line segment is arranged at the center of the N atom mark and the lower right corner of the plate, a fourth imaginary line segment is arranged at the center of the C atom mark and the lower left corner of the plate, and a fifth imaginary line segment is arranged at the center of the N atom mark and the upper right corner of the plate; the plate is provided with two through holes on two imaginary straight lines where the fourth imaginary line segment and the fifth imaginary line segment are positioned, and can be inserted into the second special module; the plate is provided with a semi-through hole on the third imaginary line segment and can be spliced with the third special module;
the main body of the second special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with a-NH mark which can be inserted into the right upper corner hole of the first special module, the long pipe with the thin disc in the rear is provided with a-CO mark which can be inserted into the left lower corner hole of the first special module, the long pipe without the thin disc is provided with a-R mark which can be inserted into the short and thick pipe of the third special module;
the main body of the third special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one pipe is long and thin, the other pipe is short and thick, and the other two pipes are respectively connected with a sphere; the long pipe of the third special module can be inserted into the right lower corner hole of the first special module or the short thick pipe of the other third special module, and the short thick pipe of the third special module can be inserted into the long pipe marked with CO of the second special module or the long pipe of the other third special module.
Preferably, in the first special module, the length of the first virtual line segment is 5.28 length units, the length of the second virtual line segment is 4.96 length units, the length of the third virtual line segment is 2.90 length units, the length of the fourth virtual line segment is 2.62 length units, the length of the fifth virtual line segment is 2.42 length units, and the inner diameters of the two through holes and the one half through hole are 1.6 length units; an included angle between the first imaginary line segment and the second imaginary line segment is 121 °, an included angle between the first imaginary line segment and the third imaginary line segment is 124 °, an included angle between the first imaginary line segment and the fourth imaginary line segment is 118 °, and an included angle between the first imaginary line segment and the fifth imaginary line segment is 122 °; the top view of the first labeled special module is shown in fig. 11, and the basic theoretical data parameters of the peptide plane composed of proline are shown in fig. 10, wherein the distance between the N atom and the C α atom at the upper right corner is 0.148nm, the distance between the C α atom at the upper right corner and the C β atom is 0.154nm, the distance between the C β atom and the C γ atom is 0.151nm, and the distance between the C γ atom and the C δ atom is 0.152 nm; when the N atom is taken as the center, the included angle between the C atom and the C alpha atom at the upper right corner is 122 degrees, and the included angle between the C alpha atom at the upper right corner and the C delta atom is 113 degrees; when the C alpha atom at the upper right corner is taken as the center, the included angle between the N atom and the CO group is 111 degrees, and the included angle between the N atom and the C beta atom is 103 degrees; when the C beta atom is taken as the center, the included angle between the C alpha atom at the upper right corner and the C gamma atom is 105 degrees; when the C gamma atom is taken as the center, the included angle between the C beta atom and the C delta atom is 106 degrees; when the C delta atom is taken as the center, the included angle between the C gamma atom and the N atom is 103 degrees;
in the second special module, the outer diameters of four pipes are 1.6 length units, the lengths of three long pipes are 5.6 length units, the long pipe with the R mark is provided with an annular mark at a position 2.24-2.36 length units away from the center of the module, the length of a short pipe is 5 length units, the diameter of a sphere is 2.96 length units, two thin discs are 3.5 length units away from the center of the module, a 360-degree scale protractor is attached to the outside, and the 0-degree line of the long pipe is positioned on a plane formed by the intersection of the two central lines; the included angle between the long tube with the-NH mark and the long tube with the-CO mark is 112.3 degrees, the included angle between the long tube with the-R mark and the long tube with the-CO mark is 111 degrees, the included angle between the long tube with the-NH mark and the long tube with the-R mark is 103 degrees, and the included angles between the short tube for connecting the ball body and the other three long tubes are 110.1 degrees; the structure diagrams of the second special module from different viewing angles are shown in fig. 12 and fig. 13.
In the third special module, the outer diameter of the slender tube is 1.6 length units, the length is 5.6 length units, and an annular mark is arranged at a position 2.24-2.36 length units away from the center of the module. The inner diameter of the short and thick pipe is 1.6 length units, the length of the short and thick pipe is 3.8 length units, the length of the other two pipes is 5 length units, and the diameter of the two spheres is 2.96 length units; the included angle of the two tubes not connected with the spheres is 104 degrees, the included angle of the two tubes connected with the spheres is 110.5 degrees, and the plane where the two tubes not connected with the spheres are located is vertical to the plane where the two tubes connected with the spheres are located; the front and right views of the third special module are shown in fig. 14 and 15.
Preferably, the model further comprises a plurality of fourth special modules, wherein:
the main body of the fourth special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space; wherein two of the tubes are long tubes, the other two of the tubes are short tubes, and the outer ends of the two short tubes are respectively connected with the ball body; the two long pipes are respectively provided with a thin disc which is vertical to the length direction of the pipes, and a protractor is attached to the outside; one of the long tubes with thin disks is provided with a-NH mark which can be inserted into the right upper corner hole of the first basic module, and the other long tube with thin disks is provided with a-CO mark which can be inserted into the left lower corner hole of the first basic module.
Preferably, in the fourth special module, the outer diameters of four tubes are all 1.6 length units, the included angle between the long tube with the-CO mapping and the long tube with the-NH mapping is 112.1 °, the included angles between the other tubes are 109 °, the lengths of two long tubes are 5.6 length units, the lengths of two short tubes are 5 length units, the diameter of the sphere is 2.96 length units, the distance between two thin discs and the center of the module is 3.5 length units, and a 360 ° scale protractor is externally attached, and the 0 ° line of the protractor is located on a plane formed by intersecting central lines of the two long tubes; a front view of the fourth special module is shown in fig. 16.
Preferably, the model further comprises a plurality of fifth special modules and a plurality of sixth special modules, wherein:
the main body of the fifth special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one pipe is long and thin, the other pipe is short and thick, and the other two pipes are respectively connected with a sphere;
the sixth special module consists of two pipes which are emitted from the center and are connected with each other and a detachable sphere, wherein one pipe is a thick pipe and can be spliced with the slender pipe of the fifth special module, and the other pipe is a thin pipe which is connected with the detachable sphere;
preferably, in said fifth special module, the four tubes are mutually inclined at an angle of 109 ° 28', the outer diameter of the elongated tube is 1.6 length units, the length is 5.6 length units, and there is a ring mark at a distance of 3.48 length units from the center of the module; the inner diameter of the short and thick tube is 1.6 length units, the length is 3.8 length units, the length of the other two tubes is 5 length units, and the diameter of the two spheres is 2.96 length units.
Preferably, in the sixth special module, the included angle between the two tubes is 104 °, the length of the thin tube is 4.1 length units, the outer diameter is 1.6 length units, the tube is a solid tube, the end of the tube is provided with a plug with the diameter of 0.35 length unit and the length of 0.86 length unit, the center of the end of the tube is used as the center, the left side and the right side of the included angle of 86.4 ° with the plug are respectively provided with a jack matched with the plug, the length of the thick tube is 3.8 length units, the inner diameter is 1.6 length units, the diameter of the sphere is 2.96 length units, and the jacks matched with the plug are arranged; the left side view of the interconnected tubes in the sixth particular module is shown in fig. 17, the front view in fig. 18, and the left side view of the removable sphere in fig. 19.
Preferably, the model further comprises a plurality of seventh special modules, wherein:
the seventh special module is the right half of the first special module, and a splicing structure which is the same as the fourth basic module and can be inserted into a third basic module is arranged at the division position; the top view of the seventh special module is shown in fig. 20.
Preferably, the model further comprises a hydrogen bonding module, wherein the hydrogen bonding module is an elongated round stick; the centers of the O atom mark and the H atom mark in the first basic module, the third basic module, the fourth basic module, the first special module or the seventh special module are also provided with circular jacks matched with the elongated circular sticks;
preferably, the diameter of the slender round stick is 0.15 length units, and the length of the slender round stick is 6.5 length units; the diameter of the circular jack is 0.15 length units.
Preferably, the mark of the invention can be in any form of pictures, seal cutting, painting and the like.
Compared with the prior art, the invention has the beneficial effects that:
the invention can directly show the relationship of each atom and each adjacent chemical bond of the peptide plane, can resist repeated rotation without loosening, has stable conformation, and can directly measure or visually obtain the angle value by manufacturing the peptide plane into a plane structure to replace the traditional ball stick model, enabling the imino end and the carbonyl end to be detachable, manufacturing the linking point C alpha of the adjacent peptide plane into a ball model as a connecting pivot, and using a sleeve pipe for connecting to replace the ball stick. The invention is based on the basic data of protein structure science, builds a realistic model for any teacher according to theoretical data through the reconstruction of a peptide plane three-dimensional model, simplifies, stereoscopically, realistically and vividly teaching, facilitates the teaching of the teacher, and simultaneously improves the learning interest of students and deepens the understanding and mastering of difficult and difficult knowledge. The invention can be used for teaching tools of biochemistry and molecular biology, can also be used as scientific research tools in the research process of protein structure biology, and provides a model basis for researching a protein secondary structure. The model of the invention has simple operation and convenient assembly, and is convenient for teaching and scientific research.
The model of the invention can assemble and display various teaching contents including the following contents:
(1) peptide bonds, amino acid residues, and oligopeptides such as dipeptides and tripeptides;
(2) special amino acid proline, glycine and cysteine structures;
(3) measurement of the rotation angle and dihedral angle of the peptide plane;
(4) and the secondary structures of alpha helix, beta folding, beta rotation angle and the like of the protein.
Drawings
FIG. 1 is a graph of basic theoretical data for the positions of six atoms in the peptide plane and the corresponding bond angles and bond lengths;
FIG. 2 is a design drawing of a first basic module of the present invention;
FIG. 3 is a top plan view of a first base module of the present invention, not labeled;
FIG. 4 is a top view of the first base module of the present invention after marking;
FIG. 5 is a front view of the first base module of the present invention after marking;
FIG. 6 is a top view of a second base module of the present invention;
FIG. 7 is a front view of a second base module of the present invention;
FIG. 8 is a top view of a third base module of the present invention;
FIG. 9 is a top view of a fourth base module of the present invention;
FIG. 10 is a graph of basic theoretical data for a peptide plane consisting of proline;
FIG. 11 is a top view of the first special module of the present invention after marking;
FIG. 12 is a block diagram of a second particular module of the invention;
FIG. 13 is a block diagram of a second particular module of the invention;
FIG. 14 is a front view of a third particular module of the invention;
FIG. 15 is a right side view of a third particular module of the invention;
FIG. 16 is a front view of a fourth particular module of the invention;
FIG. 17 is a left side elevational view of interconnected tubes in a sixth particular module of the invention;
figure 18 is a front view of interconnected tubes in a sixth particular module of the invention;
FIG. 19 is a left side elevational view of a removable sphere in a sixth particular module of the invention;
FIG. 20 is a top view of a seventh special module of the invention;
FIG. 21 is a peptide bond linkage display in example 2 of the present invention;
FIG. 22 is a diagram showing amino acid residue linkages in example 2 of the present invention;
FIG. 23 is a trans-ligation of proline in example 3 of the present invention;
FIG. 24 is a cis-linked representation of proline in example 3 of the present invention;
FIG. 25 is a graph showing the basic theoretical data of cysteine side chains in example 4 of the present invention;
FIG. 26 is a view showing the linkage of disulfide bonds in example 4 of the present invention;
FIG. 27 is a view showing the connection at a rotation angle φ =180 °, ψ =0 ° of the peptide plane in example 6 of the present invention;
FIG. 28 is a connection display diagram of dihedral angles φ and ψ of 0 ° in example 7 of the present invention;
FIG. 29 is a connection diagram showing dihedral angles φ = -47 °, ψ = -57 ° in examples 7 and 8 of the present invention;
Detailed Description
The invention will be further described with reference to specific embodiments, and the advantages and features of the invention will become apparent as the description proceeds. These examples are illustrative only and do not limit the scope of the present invention in any way. It will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention, and that such changes and modifications may be made without departing from the spirit and scope of the invention.
EXAMPLE 1 determination of basic size data of a first basic Module
And (3) manufacturing the model size and the data parameters of the peptide plane teaching aid model according to the positions of six atoms of the peptide plane and the corresponding key angles and the basic theoretical data of the key lengths, so as to determine the size of the first basic module, wherein the key angles are unchanged, and the key lengths can be scaled in equal proportion.
FIG. 1 is a diagram of basic theoretical data of the positions of six atoms in a peptide plane and corresponding bond angles and bond lengths, wherein the distance between a C atom and a N atom is 0.132nm, the distance between a C atom and an O atom is 0.123nm, the distance between a N atom and an H atom is 0.101nm, the distance between a C atom and a C α atom at the lower left corner is 0.153nm, and the distance between a N atom and a C α atom at the upper right corner is 0.147 nm; when the C atom is taken as the center, the included angle between the N atom and the O atom is 123.5 degrees, and the included angle between the N atom and the C alpha atom at the lower left corner is 116 degrees; when the N atom is taken as the center, the included angle between the C atom and the H atom is 120 degrees, and the included angle between the C atom and the C alpha atom at the upper right corner is 122 degrees.
Fig. 2 is a design diagram of a first basic module.
Example 2 Assembly and display of peptide bonds, amino acid residues and oligopeptides such as dipeptides, tripeptides and the like Using the third, fourth and fifth base modules
Peptide bonds are formed by dehydration condensation of the alpha amino group of one amino acid with the alpha carboxy group of another amino acid, and are displayed and assembled by the third basic module (carbonyl-terminal module) and the fourth basic module (imino-terminal module) through an intermediate splicing structure, as shown in fig. 21. Since the peptide chain amino acids exist as residues, the amino acid residues can be assembled from the fourth basic module (imino-terminal module), the fifth basic module (ca-module), and the third basic module (carbonyl-terminal module) in the order from left to right as shown in FIG. 22. The basic assembly method of the oligopeptide: a fourth base module-a fifth base module-a third base module-a fourth base module-a fifth base module-a third base module … …, thereby displaying the primary structure of the protein.
Example 3 Assembly and display of peptide bonds formed by the amino acid end of proline Using the third basic Module, the seventh Special Module, the second Special Module and the third Special Module
Proline is an imino acid, and a residue model of the proline is composed of a proline-specific peptide plane module, a proline alpha carbon structure module and 3 proline side chain carbon structure modules. The proline-specific detachable module can assemble and display a peptide bond structure formed by proline amino acid ends, wherein proline can also form a trans connection and a cis connection, which are respectively shown in fig. 23 and fig. 24.
Preparing a third basic module, a seventh special module, a second special module and three third special modules, and assembling according to the following method:
(1) inserting a long pipe marked with-NH in the second special module into a right upper corner hole of the seventh special module;
(2) inserting the long pipe marked with-R in the second special module into the short thick pipe of the first third special module;
(3) inserting the elongated tube of a first third special module into the short and thick tube of a second third special module;
(4) inserting the elongated tube of a second third special module into the short and thick tube of the third special module;
(5) inserting the elongated tube of a third special module into a right lower corner hole of a seventh special module, rotating the connection parts at the moment, and gradually finely adjusting the direction and the depth until the elongated tube is inserted into the annular mark;
(6) if the seventh special module is inserted face-on into the third basic module, the trans configuration as shown in fig. 23 can be obtained; if the seventh special module is inserted in the third basic module on the reverse side, the cis configuration as shown in FIG. 24 can be obtained.
Example 4 Assembly and display of peptide bonds formed by the amino acid end of Glycine Using the first basic Module and the fourth Special Module
The glycine has no side chain carbon structure but hydrogen atom, and the carbon-hydrogen bond length is short, so that a special glycine module C is specially designed.
Preparing a first basic module and a fourth special module, and assembling according to the following method:
the long tube marked with-NH in the fourth special module is inserted into the right upper corner hole of the first basic module.
Example 5 Assembly and display of cysteine side chains Using the second basic Module, the fifth Special Module, the sixth Special Module
The main structural parameters of the cysteine side chain are shown in fig. 25, wherein the distance between the C α atom and the C β atom is 0.154nm, the distance between the C β atom and the S atom is 0.182nm, and the distance between the S atom and the H atom is 0.135 nm; when the C beta atom is taken as the center, the included angle between the C alpha atom and the S atom is 109 degrees and 28 degrees; when S atom is taken as the center, the included angle between C beta atom and H atom is 104.
Preparing a second basic module, a fifth special module and two sixth special modules, and assembling according to the following method:
(1) inserting the long pipe marked with-R in the second basic module into the short thick pipe of the fifth special module to the annular mark of the-R pipe;
(2) inserting the slender tube of the fifth special module into the thick tube of the first sixth special module to the annular mark of the slender tube, and inserting the plug at the tail end of the slender tube into the jack of the sphere representing the hydrogen atom to form a cysteine side chain;
(3) when two cysteine links are required, the spheres representing hydrogen atoms in the two sixth special modules are removed and the ends of the two tubules are then spliced to each other to form a disulfide bond. The tail end of each thin tube is provided with a plug and two jacks, two rotating directions can be inserted, the two jacks and the plug are separated by 86.4 degrees, and the S-C keys on two sides can be ensured to be vertical to each other by forming a key angle of 104 degrees with the two keys of the S atom. As shown in fig. 26.
Example 6 rotation angles of peptide planes assembled and displayed using first and second base modules
The phi and psi angles of adjacent peptide planes can be displayed using the disc protractors provided in the model of the invention. Two adjacent peptide units are arranged from the amino (N) end to the carboxyl (C) end, and atoms on the peptide chain are coded as C alpha 1-C1-N1-C alpha 2-C2-N2 from the first alpha-carbon atom, and belong to the main chain framework atoms of the peptide chain. When the C α 2-C2 bond is in cis configuration with the C1-N1 bond, Φ =0 °, in trans configuration Φ = ± 180 °; viewing from the C α 2 end along the N1-C α 2 key axis, φ increases when the key is rotated clockwise and φ decreases when rotated counterclockwise. ψ =0 ° when the N1-C α 2 bond is in cis with the C2-N2 bond, ψ = ± 180 ° in trans; viewed from the end of C α 2 along the key axis C α 2-C2, the keys increase in clockwise rotation ψ and decrease in counterclockwise rotation ψ.
Method for assembling and displaying the rotation angle of a peptide plane using one first and two second basic modules:
(1) inserting a long pipe marked with-NH in the first second basic module into the right upper corner hole of the first basic module;
(2) the long tube labeled-CO in the second base module was inserted into the lower left corner hole of the first base module.
The angle of the protractor at the-NH end on the first second basic module corresponding to the triangular mark tip at the upper right corner of the plate plane of the first basic module is phi, and represents the rotation angle of the C alpha-N single bond; the angle of the triangle mark tip at the lower left corner of the plate plane of the first basic module corresponding to the protractor at the-CO end of the second basic module is psi, and represents the rotation angle of the C alpha-C single bond.
And when the C alpha structure is seen to the peptide plane, the clockwise rotation of the plane is positive, and the anticlockwise rotation of the plane is negative, and specifically, the scale corresponding to the intersection of the peptide plane and the protractor is seen.
When Φ =180 °, ψ =0 °, as shown in fig. 27.
Example 7 assembly and demonstration of the measurement of phi and psi dihedral angles using a first and a second base module
Method for assembling and displaying the rotation angle of a peptide plane using two first and one second basic modules:
(1) inserting a long pipe marked with-NH in the second basic module into the right upper corner hole of the first basic module;
(2) the long tube labeled-CO in the second base module was inserted into the lower left corner hole of the second first base module.
First, it is necessary to clarify the definition of 0 °, which is shown in fig. 28, when determining the rotation angle Φ of ca-N, if N-C at both ends thereof is coplanar with ca-C and on the same side thereof (cis), then Φ is 0 ° when looking from the α carbon atom to N, clockwise is a positive angle, and counterclockwise is a negative value. The definition of psi can be known in the same way. When the first basic module is rotated, the edge at the insertion pipe port of the first basic module rotates along the disc surface of the protractor, starting from the 0-degree position, clockwise is positive, and anticlockwise is negative, and the scale corresponding to the edge is the rotation angle.
When Φ = -47 °, ψ = -57 °, as shown in fig. 29.
Example 8 Assembly and display of the Secondary Structure of proteins alpha helix and beta sheet Using first, second and Hydrogen bonding modules
Pauling and Corey suggested that alpha helices (α -helix) and β sheets (β -pleated sheet) are the major forms of protein secondary structure based on experimental data.
1. Secondary structure alpha helix of proteins
In the alpha helix structure, the polypeptide chain backbone rises spirally about a central axis, the helix runs in a clockwise right-handed helix with a phi angle of-47 DEG, a psi angle of-57 DEG, and the side chain R groups of the amino acid extend outside the helix, depending on the direction of the peptide chain from the amino terminus (N-terminus) to the carboxy terminus (C-terminus). Every 3.6 amino acid residues spirally ascends one turn (i.e., rotates 360 °), and the pitch is 0.54 nm. The N-H of each peptide bond of the alpha helix and the carbonyl oxygen of the fourth peptide bond form a hydrogen bond, the direction of which is substantially parallel to the long axis of the helix. All of the carbonyl oxygens in all peptide bonds in the peptide chain can form hydrogen bonds to stabilize the alpha helical structure.
A method for assembling and displaying a secondary structure alpha helix of a protein using a plurality of first building blocks, a plurality of second building blocks, and a plurality of hydrogen bonding blocks:
(1) inserting a long tube marked with-NH in a second basic module into a right upper corner hole of a first basic module;
(2) inserting a long tube marked with-CO in one second basic module into a left lower corner hole of the other first basic module;
(3) the phi angle is adjusted to be-47 degrees, and the psi angle is-57 degrees (as shown in figure 29);
(4) repeating the steps (1) to (3) and continuing to extend;
(5) a hydrogen bonding module is inserted between the circular insertion hole on the H atom mark in each first base module and the circular insertion hole on the O atom mark in the fourth first base module from the beginning thereof to stabilize the α -helical structure.
2. Beta sheet of secondary structure of proteins
Beta folding is in a paper folding shape, polypeptide chains are fully extended, each peptide plane (peptide unit) takes the C alpha as a rotation point, the peptide planes are sequentially folded to be in a sawtooth structure, amino acid residue side chains are alternately positioned above and below the sawtooth structure, the sawtooth structures of a plurality of peptide segments in one peptide chain can be arranged in parallel, two peptide segments which are far away from each other in a molecule can form the same trend through folding, and also can form the opposite trend through folding.
A method for assembling and displaying a secondary structure beta sheet of a protein using a plurality of first building blocks, a plurality of second building blocks, and a plurality of hydrogen bonding blocks:
(1) inserting a long tube marked with-NH in a second basic module into a right upper corner hole of a first basic module;
(2) inserting a long tube marked with-CO in one second basic module into a left lower corner hole of the other first basic module;
(3) adjusting phi angle to-140 degrees and psi angle to 130 degrees;
(4) repeating the steps (1) to (3) and continuing to extend;
(5) a hydrogen bonding module is inserted between the circular insertion hole on the H atom mark in each first basic module and the circular insertion hole on the H atom mark in the adjacent first basic module to show the effect of hydrogen bonding on stabilizing the beta sheet structure.
Claims (13)
1. A model of a modular assembly peptide chain spatial structure, the model comprising a plurality of first base modules and a plurality of second base modules, wherein:
the main body of the first basic module is a plate, the position of the center of the plate, which is towards the left, is provided with a C atom mark, the position of the center of the plate, which is towards the right, is provided with an N atom mark, the position of the upper left corner of the plate is provided with an O atom mark, and the position of the lower right corner of the plate is provided with an H atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark is arranged between the N atom mark and the H atom mark, a single bond mark and a triangular mark are arranged at the left lower corner of the C atom mark and the plate, and a single bond mark and a triangular mark are arranged at the right upper corner of the N atom mark and the plate; a first imaginary line segment is arranged at the center of the C atom mark and the center of the N atom mark, a second imaginary line segment is arranged at the center of the C atom mark and the center of the O atom mark, a third imaginary line segment is arranged at the center of the N atom mark and the center of the H atom mark, a fourth imaginary line segment is arranged at the center of the C atom mark and the lower left corner of the plate, and a fifth imaginary line segment is arranged at the center of the N atom mark and the upper right corner of the plate; the plate is provided with two through holes on two imaginary straight lines of the fourth imaginary line segment and the fifth imaginary line segment;
the main body of the second basic module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with an-NH mark, the long pipe with the thin disc in the rear is provided with a-CO mark, and the long pipe without the thin disc is provided with an-R mark.
2. The model of claim 1, wherein:
in the first basic block, the length of the first virtual line segment is 5.28 length units, the length of the second virtual line segment is 4.92 length units, the length of the third virtual line segment is 4.04 length units, the length of the fourth virtual line segment is 6.12 length units, the length of the fifth virtual line segment is 5.88 length units, and the inner diameters of the two through holes are 1.6 length units; an included angle between the first imaginary line segment and the second imaginary line segment is 123.5 °, an included angle between the first imaginary line segment and the third imaginary line segment is 120 °, an included angle between the first imaginary line segment and the fourth imaginary line segment is 116 °, and an included angle between the first imaginary line segment and the fifth imaginary line segment is 122 °;
in the second basic module, the outer diameters of four pipes are all 1.6 length units, the included angle between a long pipe with a-NH mark and a long pipe with a-CO mark is 111 degrees, the included angle between a long pipe with a-R mark and a long pipe with a-NH mark is 110.6 degrees, the included angle between a long pipe with a-R mark and a long pipe with a-CO mark is 110.6 degrees, the included angles between a short pipe connecting a sphere and three long pipes are 108.2 degrees respectively, the lengths of the three long pipes are 5.6 length units, the long pipe with a-R mark is provided with an annular mark at a position 2.24-2.36 length units away from the center of the module, the length of one short pipe is 5 length units, the diameter of the sphere is 2.96 length units, and two thin disks are 3.5 length units away from the center of the module, and a protractor with 360-degree scales is pasted outside, and the 0-degree line of the protractor is positioned on a plane formed by the intersection of the central lines of the two long pipes.
3. The model of claim 1, further comprising a plurality of third base modules and a plurality of fourth base modules, wherein:
the third basic module and the fourth basic module are respectively a left half block and a right half block of the first basic module, and the division positions are provided with inserting structures which can be inserted into each other.
4. The model of claim 1, further comprising a plurality of first special modules, a plurality of second special modules, and a plurality of third special modules, wherein:
the main body of the first special module is a plate, the position of the center of the plate, which is towards the left, is provided with a C atom mark, the position of the center of the plate, which is towards the right, is provided with an N atom mark, and the position of the upper left corner of the plate is provided with an O atom mark; a single bond mark is arranged between the C atom mark and the N atom mark, a double bond mark is arranged between the C atom mark and the O atom mark, a single bond mark and a triangular mark are arranged at the left lower corner of the C atom mark and the plate, a single bond mark and a triangular mark are arranged at the right upper corner of the N atom mark and the plate, and a single bond mark is arranged between the N atom mark and the right lower corner of the plate; a first imaginary line segment is arranged at the center of the C atom mark and the center of the N atom mark, a second imaginary line segment is arranged at the center of the C atom mark and the center of the O atom mark, a third imaginary line segment is arranged at the center of the N atom mark and the lower right corner of the plate, a fourth imaginary line segment is arranged at the center of the C atom mark and the lower left corner of the plate, and a fifth imaginary line segment is arranged at the center of the N atom mark and the upper right corner of the plate; the plate is provided with two through holes on two imaginary straight lines of the fourth imaginary line segment and the fifth imaginary line segment; the plate has a semi-through hole on the third imaginary line segment;
the main body of the second special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein three pipes are long pipes, the other pipe is a short pipe, and the outer end of the short pipe is connected with a sphere; two long tubes of the three long tubes are respectively provided with a thin disc vertical to the length direction of the tubes, and a protractor is externally attached; when the long pipe without the thin disc is placed downwards and the short pipe connected with the sphere is placed upwards towards the right side, the long pipe with the thin disc in the front is provided with an-NH mark, the long pipe with the thin disc in the rear is provided with a-CO mark, and the long pipe without the thin disc is provided with an-R mark;
the main body of the third special module is four tubes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one tube is long and thin, the other tube is short and thick, and the other two tubes are respectively connected with a sphere.
5. The model of claim 4, wherein:
in the first special module, the length of the first virtual line segment is 5.28 length units, the length of the second virtual line segment is 4.96 length units, the length of the third virtual line segment is 2.90 length units, the length of the fourth virtual line segment is 2.62 length units, the length of the fifth virtual line segment is 2.42 length units, and the inner diameters of the two through holes and the one half through hole are 1.6 length units; an included angle between the first imaginary line segment and the second imaginary line segment is 121 °, an included angle between the first imaginary line segment and the third imaginary line segment is 124 °, an included angle between the first imaginary line segment and the fourth imaginary line segment is 118 °, and an included angle between the first imaginary line segment and the fifth imaginary line segment is 122 °;
in the second special module, the outer diameters of four pipes are 1.6 length units, the lengths of three long pipes are 5.6 length units, the long pipe with the R mark is provided with an annular mark at a position 2.24-2.36 length units away from the center of the module, the length of a short pipe is 5 length units, the diameter of a sphere is 2.96 length units, two thin discs are 3.5 length units away from the center of the module, a 360-degree scale protractor is attached to the outside, and the 0-degree line of the long pipe is positioned on a plane formed by the intersection of the two central lines; the included angle between the long tube with the-NH mark and the long tube with the-CO mark is 112.3 degrees, the included angle between the long tube with the-R mark and the long tube with the-CO mark is 111 degrees, the included angle between the long tube with the-NH mark and the long tube with the-R mark is 103 degrees, and the included angles between the short tube for connecting the ball body and the other three long tubes are 110.1 degrees;
in the third special module, the outer diameter of the slender pipe is 1.6 length units, the length of the slender pipe is 5.6 length units, the annular mark is arranged at a position 2.24-2.36 length units away from the center of the module, the inner diameter of the short and thick pipe is 1.6 length units, the length of the short and thick pipe is 3.8 length units, the lengths of the other two pipes are 5 length units, and the diameters of the two spheres are 2.96 length units; the included angle of the two tubes not connected with the spheres is 104 degrees, the included angle of the two tubes connected with the spheres is 110.5 degrees, and the plane where the two tubes not connected with the spheres are located is perpendicular to the plane where the two tubes connected with the spheres are located.
6. The model of claim 1, further comprising a plurality of fourth special modules, wherein:
the main body of the fourth special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space; wherein two of the tubes are long tubes, the other two of the tubes are short tubes, and the outer ends of the two short tubes are respectively connected with the ball body; the two long pipes are respectively provided with a thin disc which is vertical to the length direction of the pipes, and a protractor is attached to the outside; one of the long tubes with the thin disks is provided with a-NH mark, and the other long tube with the thin disks is provided with a-CO mark.
7. The model of claim 6, wherein:
in the fourth special module, the outer diameters of four pipes are all 1.6 length units, the included angle between the long pipe with the-CO mapping and the long pipe with the-NH mapping is 112.1 degrees, the included angles between the other pipes are 109 degrees, the lengths of the two long pipes are 5.6 length units, the lengths of the two short pipes are 5 length units, the diameter of a sphere is 2.96 length units, the distance between the two thin discs and the center of the module is 3.5 length units, the 360-degree scale protractor is externally attached, and the 0-degree line of the protractor is located on a plane formed by intersecting center lines of the two long pipes.
8. The model of claim 3, further comprising a plurality of fifth special modules and a plurality of sixth special modules, wherein:
the main body of the fifth special module is four pipes which are emitted from the center and are mutually connected in a three-dimensional space, wherein one pipe is long and thin, the other pipe is short and thick, and the other two pipes are respectively connected with a sphere;
the sixth special module consists of two tubes which are emitted from the center and are connected with each other and a detachable sphere, wherein one tube is a thick tube, and the other tube is a thin tube which is connected with the detachable sphere.
9. The model of claim 8, wherein:
in the fifth special module, the included angle between the four tubes is 109 degrees 28 degrees, the outer diameter of the slender tube is 1.6 length units, the length is 5.6 length units, and an annular mark is arranged at a position 3.48 length units away from the center of the module; the inner diameter of the short and thick tube is 1.6 length units, the length is 3.8 length units, the length of the other two tubes is 5 length units, and the diameter of the two spheres is 2.96 length units.
10. The model of claim 8, wherein:
in the sixth special module, the included angle between the two pipes is 104 degrees, the length of the thin pipe is 4.1 length units, the outer diameter is 1.6 length units, the thin pipe is a solid pipe, the tail end of the thin pipe is provided with a plug with the diameter of 0.35 length unit and the length of 0.86 length unit, the center of the tail end of the thin pipe is used as the center, the left side and the right side of the included angle of 86.4 degrees with the plug are respectively provided with a jack matched with the plug, the length of the thick pipe is 3.8 length units, the inner diameter of the thick pipe is 1.6 length units, the diameter of the sphere is 2.96 length units, and jacks matched with the plug are arranged.
11. The model of claim 4, further comprising a plurality of seventh special modules, wherein:
the seventh special module is a right half block of the first special module, and the division is provided with a plug-in structure which is the same as the fourth basic module and can be inserted into the third basic module.
12. A model according to any of claims 1-11, further comprising a hydrogen bonding module, said hydrogen bonding module being an elongated round stick; the centers of the O atom mark and the H atom mark in the first basic module, the third basic module, the fourth basic module, the first special module or the seventh special module are also provided with circular jacks matched with the elongated round sticks.
13. The model of claim 12, wherein:
the diameter of the slender round stick is 0.15 length units, and the length of the slender round stick is 6.5 length units; the diameter of the circular jack is 0.15 length units.
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