CN104715164B - With the DNA frame position Forecasting Methodologies of protein interaction - Google Patents
With the DNA frame position Forecasting Methodologies of protein interaction Download PDFInfo
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Abstract
The present invention relates to the DNA frame position Forecasting Methodologies with protein interaction, comprise the following steps：The determination of DNA key points；DNA space conformations are searched on a large scale using coarse statistical potentials function；The conformation arrived for second step, sequence is carefully selected using the fine polarizable field of force.The present invention uses sequence analysis protein nucleic acid interface residue, and these interface residues can significantly reduce crucial lattice point, it will be apparent that improves search speed so that search is more targeted.
Description
Technical field
The present invention relates to a kind of method of computer forecast protein function, belong to biology information technology, computational methods
With computer virtual reality technology.
Background technology
The computational methods of prediction protein function mainly have four kinds：
One kind is the method based on structural similarity.This kind of method utilizes the similarity degree of three-dimensional structure, analyzes target egg
White most probable functional construction unit, searches for the protein similar to these construction units in known Protein Data Bank
Performance data, so as to reach the target of prediction target protein function.Some algorithms can not have to consider topological structure, and only consider
Space structure.But this kind of method will rely on the similar structure being currently known, be not suitable for finding new function.
One kind is the method based on three-dimensional motif.These methods are more attempt to find tool functional knot in protein
Constitutive element, such as Helix-Turn-Helix (HTH) motif being found in many DBPs.So, people are just
The function of the protein with these motifs can be obtained by similar database approximation.Such as with TESS algorithms enzyme work
The PROCAT databases that property site is set up；Directly using Protein structure databases (Protein Database Bank,
Abbreviation PDB) the PDBSite storehouses established of the site information in file etc..This kind of method equally relies on the function information being currently known,
Be not suitable for finding new function.
One kind is the method based on surface.This kind of method would generally according to the three-dimensional coordinate of each atom and from each other away from
From producing protedogenous surface, and think that the shape on these surfaces and degree identical between each other are to determine protein function
Principal element.Certainly, also there are some researches show the function of some protein is determined by the hydrophobic property or electrostatic property on surface
Fixed.This kind of method is generally called molecular docking method, is had a wide range of applications in Computer-Aided Drug Design.It is this kind of
More than the comparison that method is studied at present is small-molecule drug.
Also one kind is the method based on study.This kind of method includes data mining, artificial intelligence, and various method layers go out not
Thoroughly, SVMs, decision tree, artificial neural network etc. are used for example.They attempt to find protein in various manners
Association between the information such as the sequential structure of function information and protein（It is display or implicit）, to reach the purpose of prediction.
This kind of method is still based on existing knowledge base.Be not suitable for the unknown function of exploration discovery protein.
The content of the invention
Present disclosure is to provide what a kind of prediction being combined based on thickness scoring functions was combined with protein
The method of DNA segment.Can be on more broadly level, by finding the DNA being combined, can not even to pass through experimental identification function
Albumen provide reference and theoretical foundation.
The used to achieve the above object technical scheme of the present invention is：With the DNA frame positions of protein interaction
Forecasting Methodology, comprise the following steps：
Nucleic acid interface residue information is obtained by dp-bind softwares according to protein sequence；
Three-dimensional system of coordinate where target protein is split to form cube lattice point by setting length；Visited using coarse
Pin calculates energy on the cube lattice point around target protein, and records lattice site and energy；Lattice are screened according to energy
Point is determined as the position candidate for placing DNA starting points, only retains and is less than threshold value in setpoint distance self-energy apart from interface residue
Lattice point is as crucial lattice point；
The search for clicking through beginning-of-line and direction to critical square with reference to DNA conformational characteristics obtains alternative DNA frame positions, and adopts
Screen to obtain DNA frame positions with statistical potentials coarse function；Sequence screening is carried out by the polarizable field of force again to obtain finally
The sequence of frame position.
The search that the feature of the combination DNA conformations clicks through beginning-of-line and direction to critical square comprises the following steps：
Critical square point is traveled through using the DNA double chain comprising 10 pairs of nucleotides；
All crucial lattice points are selected as starting point p, direction of key point of the chosen distance in setting range to composition
v；
It is overall around starting point axle anglec of rotation θ according to DNA start position p, direction v, DNA1；
In start position p, direction v, anglec of rotation θ1On the basis of fixation, DNA is overall further around the DNA central shaft anglecs of rotation
θ2, obtain alternative frame position.
It is described and screen to obtain DNA frame positions using statistical potentials coarse function and comprise the following steps：
Alternative DNA frame positions are subjected to bone framework image search using statistical potentials coarse function, i.e. statistical potentials are thick
Several minimum DNA skeletons of functional value are granulated as DNA frame positions.
The sequence that final DNA frame positions are obtained by polarizable field of force progress sequence screening comprises the following steps：
Binding sequence is found on the frame position that each is screened, i.e., in numerous composite sequences, using can
Polarized force field calculates energy, and selection combines 10 minimum sequences of energy value as candidate sequence.
The invention has the advantages that and advantage：
1. the present invention uses sequence analysis protein nucleic acid interface residue, the sequencing results and structural information are combined.
These interface residues can significantly reduce crucial lattice point, it will be apparent that improve search speed so that search is more targeted.
2. the fineness that the present invention can search for according to the size installation space of protein, it can suitably adjust the energy of key point
Span angular discretization precision, relatively good conformation is obtained according to current problem from threshold values.
3. of the invention can quickly find the position that may combine DNA, enter according to given protein three-dimensional structure information
And possible sequence is analyzed on this skeleton.
4. the method that the present invention provides reference for protein others functional analysis from now on, and then can attempt to explore
The RNA and polypeptide that target protein may combine.
Brief description of the drawings
Fig. 1 is flow chart of the method for the present invention；
Fig. 2 is target protein interface residue and low energy lattice point analysis chart；
Fig. 3 is DNA tile structure figures.
Embodiment
Below in conjunction with the accompanying drawings and embodiment the present invention is described in further detail.
Nature one co-exists in 20 kinds of amino acid, and DNA includes 4 kinds of bases.In DNA growth process, selection forms DNA's
Four bases are as fragment storehouse basis.The avtive spot of every kind of base is the P atoms in base, and the O3 ' of new fragment can be connect
Onto the P atoms of old molecule.In view of computation complexity, we do not recommend the oversize of growth.Recommend to exist at most in nature
B-form DNA structure.Whole flow process is largely divided into three parts.
First：The determination of DNA key points.
Second：DNA space conformations are searched on a large scale using coarse statistical potentials function.
3rd：For second obtained conformation, carefully selected using the fine polarizable field of force.
Specifically include following steps：
Nucleic acid interface residue information is obtained by dp-bind softwares according to protein sequence；
The minimum bounding box of protein structure is found first, and then this box is to external expansionObtain one bigger
Bounding box.This big bounding box is cut into small cube, the length of side isThe summit of small cubes will be put as lattice point
Put different coarse probes.Thus we have obtained the uniform discrete lattice point around protein.It is anticipated that energy lattice
Point attribute can reflect the physical property of protein.Energy, phase are being calculated around target protein on lattice point using coarse probe
Energy is closed to be recorded in lattice point attribute.Lattice point is screened according to energy（I.e. energy is less than the lattice point of threshold value）It is determined as and places DNA
The position candidate of starting point,；Delete apart from nucleic acid interface residue hypertelorism and excessively near lattice point.We only retain residual apart from interface
Cardinal distance fromLow energy lattice point.Last remaining lattice point we be referred to as crucial lattice point.
The nucleic acid interface residue information be analyzed using protein sequence data possible combination nucleic acid interface it is residual
Base, related software are dp-bind.The nucleic acid interface residue information for predicting next in software is used into low spot around target protein
In screening.
The lattice point attribute includes lattice site and energy；The lattice site can use eight angles of lattice point square
Position.
Then, the search in beginning-of-line and direction is clicked through to critical square with reference to DNA conformational characteristics, obtains alternative DNA skeletons position
Put, and screen to obtain DNA frame positions using statistical potentials coarse function；Sequence screening is carried out by the polarizable field of force again to obtain
To the optimal sequence of corresponding frame position.
The search that the feature of the combination DNA conformations clicks through beginning-of-line and direction to critical square comprises the following steps：
Critical square point is traveled through using the DNA double chain comprising 10 pairs of nucleotides；Select all crucial lattice point conducts
Starting point, it is contemplated that the tightness degree that DNA and target protein combine, we exist at a chosen distanceBetween key
Direction of the point to composition.The selection of spatial degrees of freedom：DNA start position p, direction v, the overall angle around starting point axial-rotation
（θ1）, on the basis of first three is fixed, then the overall angle around the rotation of DNA central shafts（θ2）.Simply O5 probes are taken to illustrate
This four parameters.DNA start position p is exactly the low energy lattice point closer apart from interface residue above said, direction v is DNA
Axial vector, θ1The axle surrounded is that starting point is the axle that p directions are v, θ2The axle surrounded is DNA central shaft.By aforementioned four certainly
By obtaining initial scaffold position after the search spent.
Statistical potentials coarse function is used in bone framework image search, is entered in the search of sequence using the polarizable field of force
OK, comprise the following steps：
It is to use statistical potentials coarse function vcfire in the screening of skeleton.Details may be referred to paper " An
all-atom knowledge-based energy function for protein-DNA threading,docking
decoy discrimination,and prediction of transcription-factor binding
profiles”。
We use the more accurate polarizable field of force on sequence screening.Frame position is chosen for each,
We are found on this skeleton and combine critical sequences, and in numerous composite sequences, energy, choosing are calculated using the polarizable field of force
Most stable of 10 sequences are selected as candidate sequence.
It is described and screen to obtain DNA frame positions using statistical potentials coarse function and comprise the following steps：
Alternative DNA frame positions are subjected to bone framework image search using statistical potentials coarse function, statistical potentials are thick
Several minimum DNA skeletons of granulation functional value remain, and further do sequence search on corresponding skeleton.
The sequence that final DNA frame positions are obtained by polarizable field of force progress sequence screening comprises the following steps：
Binding sequence is found on the frame position that each is screened；In numerous composite sequences, using can pole
Change the field of force and calculate energy, selection combines 10 minimum sequences of energy value as candidate sequence.
The present invention be by following proposal be realize：
1. an algorithm characteristic is by the result and three-dimensional structure energy information knot of sequence prediction protein nucleic acid interface residue
Fruit is combined, and DNA key point may be combined by finding protein surface.
Go out the interface residue of possible combination nucleic acid first by protein sequence analysis, related software is dp-bind.Will
The nucleic acid interface residue information come is predicted in software to use around target protein in the screening of low energy point.Such as to specified sequence
The fasta files of row
>XXXX:A|PDBID|CHAIN|SEQUENCE
PPGTPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGL
IEKKSKNSIQWKGVGP
Result using dp-bind software predictions is as follows：The information that wherein we use is first row and last row.The
One row POS represents the Sequence position numbers of residue, and what RES row represented is residue type, S_LBL S_PRB K_LBL K_PRB
P_LBL P_PRB row represent three kinds of different Forecasting Methodologies and corresponding prediction result respectively.MAJ_CON STR_CON are comprehensive
Three kinds of methods above determine interface residue, and wherein we only select last columns value as residue corresponding to 1 those rows
Numbering.
It is recorded in using coarse probe in lattice point attribute calculating energy, correlation energy around target protein on lattice point.
Low energy lattice point is filtered out to be provided with determining the DNA sites that may be combined.In order that the probe fastest, we often take must be calculated
Be deoxynucleotide O5 atoms come represent correlation nucleotides.Target protein is usually using full atom model.Each lattice point
On will calculate 4 kinds of nucleotides coarse probe energy.Attribute of the correlation energy as lattice point.Generally we select four kinds
Minimum energy value does follow-up processing in nucleotides.
Distance is deleted in all low energy lattice points and adjusts the lattice point of interface residue too far.Last remaining lattice point we claim
For crucial lattice point.
As shown in Fig. 2 RED sector is the prediction of interface residue.The part of figure Green represents to predict the lattice for carrying out low energy
Point.What blue portion represented is protein.The energy information of space lattice and based on sequence interface residue prediction be combined, meeting
More effectively find out the critical sites with reference to DNA.
2. combining the feature of DNA conformations, the search in beginning-of-line and direction is clicked through to analyzing the critical square come,
We mainly consider B-form DNA structural parameters, use length to be combined for 10 DNA double chain fragment with target protein.It is de-
Oxygen ribonucleic acid has a variety of different conformations, and the difference between some of which conformation constructively is simultaneously little.Pick out at present
The conformation come includes：A-DNA, b form dna, C-DNA, D-DNA, E-DNA, H-DNA, L-DNA, P-DNA and Z-DNA.But with existing
For some biosystems, visible only A-DNA, b form dna and Z-DNA in nature.Using Type B it is thin in three kinds of major confonnationals
Most common type in born of the same parents.We select length mainly to consider that this length is almost one spiralization cycle of b form dna for 10, than
More representative, another aspect is that the DNA amounts of calculation of this length are more moderate.
Play all crucial lattice point of point selection, direction is any two lattice point conformation into vector direction.In view of DNA and mesh
The tightness degree that protein combines is marked, we exist at a chosen distanceBetween point to the direction of composition.So
The benefit done is to can guarantee that DNA both ends all distance objective protein is compact, meets the natural category of protein DNA complexes
Property.And irrational conformational space can be excluded with very effective.
The selection of spatial degrees of freedom：How DNA starting point, direction select, the overall angle around starting point axial-rotation（θ1）,
On the basis of first three is fixed, then the overall angle to central shaft rotation（θ2）.Although DNA in structure for be harder
, but can't simply regard a column structure as.Even if axial original position is determined, and axially direction,
DNA pivotings can still produce different conformations.Because it is contemplated that starting point be not axial starting point, but coarse
Nucleotides starting point, so comparatively to increase a rotational freedom.Fig. 3 is a DNA fragment structure.Related piece
Section pivoting can produce different fragments.
3. on energy balane, employ statistical potentials coarse method and the fine polarizable field of force is combined.
With statistical potentials coarse function it is coarse scoring model in the screening of skeleton.Target protein uses full atom
Structural model, atomic structure coordinate data mainly obtain from Protein structure databases PDB.Its corresponding atomic type such as following table institute
Show.
Table 1
(1) the statistical potentials function of coarse：
To the albumen for training potential function, all interatomic distances are traveled through in RcutoffWithin atom pair, distance is existed
(r, r+ Δ r] atom pair in section is according to the atomic type i in its respective objects albumen and corresponding prediction albumen, DNA or RNA
In coarse atomic type j statistics be Nobs(i,j,r).By it with it is desirable that Distribution Value compared with, we can obtain
Atomic type to i, j (r, r+ Δ r] energy value of distance is：
Wherein
For NobsAtomic type is full atom model to corresponding one, two atoms in (i, j, r)
And another is the part of Coarse grained model；R represents the distance between two atoms.rcutRepresent definition blocks distance, surpasses
The atom pair for crossing this distance does not consider further that.Δ r represents the thickness of spherical shell.rαIn α be that a constant can take 1.61.R tables
Show ideal gas constant.T represents absolute temperature.fV(r) represent in all atom pairs, protein atomic and coarse probe
The ratio that atom occupies.Represent to NobsThe amendment of (i, j, r), because the atom pair actually observed may
It is fewer, influence result of calculation.N0=75.Pc(i, j, r) can simply regard energy as, but not subtract reference state.
(2) albumen for being used to train is obtained by PDB websites.Each structure is to own in PDB storehouses, and it is homologous to remove 35%
Property, its PDB ID is listed as follows shown in table.
Table 2
We use the more accurate polarizable field of force on sequence screening.On the basis of conformation has been obtained, Wo Menhui
Further analytical sequence information.We are scanned for using the current accurately polarizable field of force of comparing to DNA sequence.For
The DNA sequence dna that one length is 10, the quantity of its sequence is fnum=410=1048576.An it may be seen that backbone structure
More than 100 ten thousand sequence will be corresponded to.In order to improve calculating speed, we attempt to decompose energy, calculate each position respectively
The 4 pairs of bases and the energy of target protein put, it is as follows then to form an energy scale.Looked for finally by the form tabled look-up
To several sequences of energetic optimum.
Table 3
| pos1 | pos2 | pos3 | pos4 | pos5 | pos6 | … | pos10 | |
| AT | E | E | E | E | E | E | … | E |
| TA | E | E | E | E | E | E | … | E |
| GC | E | E | E | E | E | E | … | E |
| CG | E | E | E | E | E | E | … | E |
The DNA algorithms that may be combined around prediction target protein are characterized in sequence analysis and three-dimensional protein energy
Information is combined.Statistical potentials coarse mode Fast Evaluation is used in scoring functions in large-scale problem, fine
Part is evaluated using the polarizable field of force, is decomposed energy and is avoided multiple shot array.Concretely comprise the following steps：
Sets target protein.
Sequence analysis protein nucleic acid interface residue is first used, these interface residues can significantly reduce crucial lattice point, hence it is evident that
Raising search speed so that search it is more targeted.
The fineness searched for according to the size installation space of protein, it can suitably adjust the energy valve of key point judgement
Value, to θ1θ2The angle of discretization be adjusted, if it is desired to obtaining relatively good conformation just needs to heighten angular discretization essence
Degree, reduce the threshold values of key point.
Claims (3)
1. the DNA frame position Forecasting Methodologies with protein interaction, it is characterised in that comprise the following steps：
Nucleic acid interface residue information is obtained by dp-bind softwares according to protein sequence；
Three-dimensional system of coordinate where target protein is split to form cube lattice point by setting length；Existed using coarse probe
Energy is calculated on cube lattice point around target protein, the coarse probe of 4 kinds of nucleotides will be calculated on each lattice point
Energy, and record lattice site and energy；Minimum energy value does follow-up processing in four kinds of nucleotides of selection；Sieved according to energy
Select lattice point to be determined as the position candidate for placing DNA starting points, only retain small in setpoint distance self-energy apart from nucleic acid interface residue
In threshold value lattice point as crucial lattice point；
Beginning-of-line is clicked through to critical square with reference to DNA conformational characteristics and the search in direction obtains alternative DNA frame positions, and using system
Meter potential energy coarse function screens to obtain DNA frame positions；Sequence screening is carried out by the polarizable field of force again and obtains final DNA bones
The sequence of rack position；
The search that the feature of the combination DNA conformations clicks through beginning-of-line and direction to critical square comprises the following steps：
Critical square point is traveled through using the DNA double chain comprising 10 pairs of nucleotides；
All crucial lattice points are selected as starting point p, direction v of key point of the chosen distance in setting range to composition；
It is overall around starting point axle anglec of rotation θ according to DNA start position p, direction v, DNA1；
In start position p, direction v, anglec of rotation θ1On the basis of fixation, DNA is overall further around DNA central shaft anglecs of rotation θ2, obtain
To alternative DNA frame positions.
2. according to claim 1 and protein interaction DNA frame position Forecasting Methodologies, it is characterised in that：Institute
State to screen to obtain DNA frame positions using statistical potentials coarse function and comprise the following steps：
Alternative DNA frame positions are subjected to bone framework image search, i.e. statistical potentials coarse using statistical potentials coarse function
Several minimum DNA skeletons of functional value are as DNA frame positions.
3. according to claim 1 and protein interaction DNA frame position Forecasting Methodologies, it is characterised in that：Institute
State and carry out sequence screening by the polarizable field of force and obtain the sequences of final DNA frame positions comprising the following steps：
Binding sequence is found on the frame position that each is screened, i.e., in multiple composite sequences, uses polarizable power
Field computation energy, selection combine sequence of the 10 minimum sequences of energy value as final DNA frame positions.
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