CN101051335A - Method for simulating protein interaction using computer - Google Patents
Method for simulating protein interaction using computer Download PDFInfo
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Abstract
A method of utilizing computer to simulate interaction of protein includes preparing protein structure in PDB databank to be proper study system, carrying out energy minimization treatment on said system, heating said system up to set temperature then carrying out multi-step balance treatment on said system, executing molecular dynamic simulation on said system and studying protein amino acid residual base acted as key function in atom movement race and confirmation variation as well as variation process under set conditions.
Description
Technical field
The present invention relates to a kind of method of utilizing the computer simulation protein interaction, relate in particular to interactional method between the transcription factor of a kind of NAMD_2.6 of utilization and VMD-1.8.5 software study protein.
Background technology
Protein interaction is the committed step of vital movement process, as the transduction of synthetic, the molecular recognition of coordinated regulation, Protein Folding and the enzyme of many transcription factors and signaling molecule, immune response etc.Conventional experimental technique adopts the assaying reaction equilibrium constant to detect bond strength between the protein, also can pass through atomic force microscope, and unimolecule is operated, and protein is separated from each other provides information for dissociation process.But be the assaying reaction equilibrium constant or operate the non-bonded interaction that all can not well disclose between protein, and the method for molecular dynamics simulation can remedy above-mentioned deficiency with atomic force microscope.Moreover, can also obtain the detailed process (movement locus of each atom) of protein interaction and the many important dynamics parameters in this process by molecular dynamics simulation.
From McCammon J.A. in 1977 etc. so far first with the method research protein of molecular dynamics, the computing method of molecular dynamics simulation develop rapidly, the yardstick of the system of simulation from the yardstick of hundreds of initial several psecs of atom to more than 260 ten thousand an atom hundreds of nanosecond of today, the object of simulation comprises protein, DNA, RNA etc.But, the process of these molecular dynamics simulations is mostly finished at mainframe computer or HLRS, and utilize NAMD_2.6_Linux-i686 software for calculation and VMD-1.8.5 analysis software on PC, to carry out molecular dynamics simulation, do not appear in the newspapers both at home and abroad at present.
Summary of the invention
At the deficiencies in the prior art, the problem to be solved in the present invention provides a kind of NAMD_2.6_Linux-i686 of utilization software for calculation and VMD-1.8.5 analysis software (http://www.ks.uiuc.edu/Research/namd/) in the interactional method of ordinary PC patrix albuminoid.
Method of the present invention, carry out as follows:
(1) obtains to contain the protein structure of one or more peptide chain from the PDB database;
(2) utilize VMD-1.8.5 software to extract the target peptide chain of desire research, it is dissolved in the rectangular parallelepiped water tank (Water Box) that fills 0.9%NaCl solution, and making its minor increment apart from each wall of water tank is 10 , obtain peptide-salt solusion system, this system is made the structure that contains the non-hydrogen atom spatial position data, called after ionized.pdb makes the structure that contains hydrogen atom and hydrogen bonding parameter with this system simultaneously, called after ionized.psf;
(3) utilize NAMD_2.6_Linux-i686 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned peptide-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 20 psecs (ps) is handled, per 2 femtoseconds (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , it is the centre of sphere with each atom once that every 4fs calculates, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 , after finishing, calculating obtains the movement locus of each atom, called after minimize.dcd;
(4) then, fixing all atoms in the peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use the time of Langevin dynamics (Langevin Dynamics) temperature control method heating 20ps, system heats up gradually and is stabilized to 280-320K as a result, obtain the movement locus of each atom in this process, called after heat.dcd;
(5) use 100kcal/mol successively
2, 50kcal/mol
2, 20kcal/mol
2With 10kcal/mol
2Harmonious effect of contraction (Harmonic Constraint) retrain above-mentioned peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 300K, pressure is controlled at 1atm, difference equilibrium system 20ps, obtain the movement locus of all atoms in each step successively respectively, distinguish called after equ100.dcd, equ50.dcd, equ20.dcd and equ10.dcd successively;
(6) harmony to peptide chain retrains in the removal (5), adopt the field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the temperature-control pressure-control method identical with (5), PME grid (the Particle Mesh Ewald grid) length of side is set to 1 ± 0.1 , utilize PME long-range electric field force computing method, all hydrogen-oxygen bond distance in the fixed system, whole system is carried out the molecular dynamics simulation of 2 nanoseconds (ns), obtain the movement locus of each atom in this process, called after simulate.dcd;
(7) result of calculation minimize.dcd, heat.dcd, equ100.dcd, equ50.dcd, equ20.dcd, equ10.dcd and simulate.dcd in above-mentioned (3)-(6) are written into the movement locus of all atoms of VMD-1.8.5 software observes;
(8) the conformation change process by above-mentioned movement locus analysing protein;
(9) find out the amino acid residue that plays a crucial role in the protein conformation change procedure.
In the above-mentioned method of utilizing the computer simulation protein interaction: the system equilibrium temperature described in the step (4) is preferably 310K.
The simulation that utilizes method of the present invention to carry out protein interaction is compared with classic method has obvious superiority:
(1) to the computational accuracy height of Van der Waals force and electric field force, computer capacity is respectively 10 and 12 , and classic method is mostly used 9 ;
(2) do not need by means of mainframe computer and HLRS, equipment requirements is low, can carry out on common PC;
(3) cpu busy percentage height, utilization factor can reach more than 95% under the situation that does not have interference;
(4) short during used machine, get final product for system about week age on the PC of double-core Pentium4 3.0G Hz processor, 1G internal memory, Redfleg Desktop 5.0 operating systems of 30,000 to 40,000 atoms;
(5) result accurately and reliably;
(6) be convenient in the life science relevant with the protein dynamics behavior and physical chemistry and field of medicaments widespread use with molecular recognition.
Description of drawings
The initial state of Fig. 1 HMG domain and POUs domain and final state conformation
A is the relative position and the conformation of the POUs domain of the HMG domain of Sox and Oct4 before the simulation among the figure, and B is both relative position and conformation (HMG domain in the above, the POUs domain below) after the simulation.
Embodiment
The invention will be further described below in conjunction with embodiment:
Embodiment 1:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the protein structure called after 1o4x.pdb of 1o4x;
(2) utilize VMD-1.8.5 software to extract the target peptide chain of desire research, it is dissolved in the rectangular parallelepiped water tank (Water Box) that fills 0.9%NaCl solution, and making its minor increment apart from each wall of water tank is 10 , obtain peptide-salt solusion system, this system is made the structure that contains the non-hydrogen atom spatial position data, called after 1o4x_ionized.pdb makes the structure that contains hydrogen atom and hydrogen bonding parameter with this system simultaneously, called after 1o4x_ionized.psf;
(3) utilize NAMD_2.6_Linux-i686 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned peptide-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 20 psecs (ps) is handled, per 2 femtoseconds (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , it is the centre of sphere with each atom once that every 4fs calculates, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 , after finishing, calculating obtains the movement locus of each atom, called after 1o4x_minimize.dcd;
(4) then, fixing all atoms in the peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use the time of Langevin dynamics (Langevin Dynamics) temperature control method heating 20ps, system heats up gradually and is stabilized to 310K as a result, obtain the movement locus of each atom in this process, called after 1o4x_heat.dcd;
(5) use 100kcal/mol successively
2, 50kcal/mol
2, 20kcal/mol
2With 10kcal/mol
2Harmonious effect of contraction (Harmonic Constraint) retrain above-mentioned peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 300K, pressure is controlled at 1atm, difference equilibrium system 20ps, obtain the movement locus of all atoms in each step successively respectively, distinguish called after 1o4x_equ100.dcd successively, 1o4x_equ50.dcd, 1o4x_equ20.dcd and 1o4x_equ10.dcd;
(6) harmony to peptide chain retrains in the removal (5), adopt the field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the temperature-control pressure-control method identical with (5), PME grid (the Particle Mesh Ewald grid) length of side is set to 1 ± 0.1 , utilize PME long-range electric field force computing method, all hydrogen-oxygen bond distance in the fixed system, whole system is carried out the molecular dynamics simulation of 2 nanoseconds (ns), obtain the movement locus of each atom in this process, called after 1o4x_simulate.dcd;
(7) result of calculation 1o4x_minimize.dcd, 1o4x_heat.dcd, 1o4x_equ100.dcd, 1o4x_equ50.dcd, 1o4x_equ20.dcd, 1o4x_equ10.dcd and 1o4x_simulate.dcd in above-mentioned (3)-(6) are written into the movement locus of all atoms of VMD-1.8.5 software observes;
(8) by the conformation change process of above-mentioned movement locus analysing protein, initial state and final state conformation are seen Fig. 1;
(9) find the ASP274 of the amino acid residue HMG that plays a crucial role in the protein conformation change procedure and the LYS18 of POUs.
Embodiment 2:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the protein structure called after 1JLU.pdb of 1JLU;
(2) utilize VMD-1.8.5 software to extract the target peptide chain of desire research, it is dissolved in the rectangular parallelepiped water tank (Water Box) that fills 0.9%NaCl solution, and making its minor increment apart from each wall of water tank is 10 , obtain peptide-salt solusion system, this system is made the structure that contains the non-hydrogen atom spatial position data, called after 1JLU_ionized.pdb makes the structure that contains hydrogen atom and hydrogen bonding parameter with this system simultaneously, called after 1JLU_ionized.psf;
(3) utilize NAMD_2.6_Linux-i686 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned peptide-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 20 psecs (ps) is handled, per 2 femtoseconds (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , it is the centre of sphere with each atom once that every 4fs calculates, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 , after finishing, calculating obtains the movement locus of each atom, called after 1JLU_minimize.dcd;
(4) then, fixing all atoms in the peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use the time of Langevin dynamics (Langevin Dynamics) temperature control method heating 20ps, system heats up gradually and is stabilized to 320K as a result, obtain the movement locus of each atom in this process, called after 1JLU_heat.dcd;
(5) use 100kcal/mol successively
2, 50kcal/mol
2, 20kcal/mol
2With 10kcal/mol
2Harmonious effect of contraction (Harmonic Constraint) retrain above-mentioned peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 300K, pressure is controlled at 1atm, difference equilibrium system 20ps, obtain the movement locus of all atoms in each step successively respectively, distinguish called after 1JLU_equ100.dcd successively, 1JLU_equ50.dcd, 1JLU_equ20.dcd and 1JLU_equ10.dcd;
(6) harmony to peptide chain retrains in the removal (5), adopt the field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the temperature-control pressure-control method identical with (5), PME grid (the Particle Mesh Ewald grid) length of side is set to 1 ± 0.1 , utilize PME long-range electric field force computing method, all hydrogen-oxygen bond distance in the fixed system, whole system is carried out the molecular dynamics simulation of 2 nanoseconds (ns), obtain the movement locus of each atom in this process, called after 1JLU_simulate.dcd;
(7) result of calculation 1JLU_minimize.dcd, 1JLU_heat.dcd, 1JLU_equ100.dcd, 1JLU_equ50.dcd, 1JLU_equ20.dcd, 1JLU_equ10.dcd and 1JLU_simulate.dcd in above-mentioned (3)-(6) are written into the movement locus of all atoms of VMD-1.8.5 software observes;
(8) the conformation change process by above-mentioned movement locus analysing protein;
(9) find the amino acid residue that plays a crucial role in the protein conformation change procedure.
Embodiment 3:
(1) obtaining code from PDB database (http://www.rcsb.org/pdb/home/home.do) is the protein structure called after 1HN2.pdb of 1HN2;
(2) utilize VMD-1.8.5 software to extract the target peptide chain of desire research, it is dissolved in the rectangular parallelepiped water tank (Water Box) that fills 0.9%NaCl solution, and making its minor increment apart from each wall of water tank is 10 , obtain peptide-salt solusion system, this system is made the structure that contains the non-hydrogen atom spatial position data, called after 1HN2_ionized.pdb makes the structure that contains hydrogen atom and hydrogen bonding parameter with this system simultaneously, called after 1HN2_ionized.psf;
(3) utilize NAMD_2.6_Linux-i686 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition (Periodic Boundary Conditions PBC) above-mentioned peptide-salt solusion system being carried out T.T. length is that the energy minimization (Minimize) of 20 psecs (ps) is handled, per 2 femtoseconds (fs) calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , it is the centre of sphere with each atom once that every 4fs calculates, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 , after finishing, calculating obtains the movement locus of each atom, called after 1HN2_minimize.dcd;
(4) then, fixing all atoms in the peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use the time of Langevin dynamics (Langevin Dynamics) temperature control method heating 20ps, system heats up gradually and is stabilized to 280K as a result, obtain the movement locus of each atom in this process, called after 1HN2_heat.dcd;
(5) use 100kcal/mol successively
2, 50kcal/mol
2, 20kcal/mol
2With 10kcal/mol
2Harmonious effect of contraction (Harmonic Constraint) constraint peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use Langevin dynamics (Langevin Dynamics) temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 300K, pressure is controlled at 1atm, difference equilibrium system 20ps, obtain the movement locus of all atoms in each step successively respectively, distinguish called after 1HN2_equ100.dcd successively, 1HN2_equ50.dcd, 1HN2_equ20.dcd and 1HN2_equ10.dcd;
(6) harmony to peptide chain retrains in the removal (5), adopt the field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the temperature-control pressure-control method identical with (5), PME grid (the Particle Mesh Ewald grid) length of side is set to 1 ± 0.1 , utilize PME long-range electric field force computing method, all hydrogen-oxygen bond distance in the fixed system, whole system is carried out the molecular dynamics simulation of 2 nanoseconds (ns), obtain the movement locus of each atom in this process, called after 1HN2_simulate.dcd;
(7) result of calculation 1HN2_minimize.dcd, 1HN2_heat.dcd, 1HN2_equ100.dcd, 1HN2_equ50.dcd, 1HN2_equ20.dcd, 1HN2_equ10.dcd and 1HN2_simulate.dcd in above-mentioned (3)-(6) are written into the movement locus of all atoms of VMD-1.8.5 software observes;
(8) the conformation change process by above-mentioned movement locus analysing protein;
(9) find out the amino acid residue that plays a crucial role in the protein conformation change procedure.
Claims (2)
1. method of utilizing the computer simulation protein interaction, carry out as follows:
(1) obtains to contain the protein structure of one or more peptide chain from the PDB database;
(2) utilize VMD-1.8.5 software to extract the target peptide chain of desire research, it is dissolved in the rectangular parallelepiped water tank that fills 0.9%NaCl solution, and making its minor increment apart from each wall of water tank is 10 , obtain peptide-salt solusion system, this system is made the structure that contains the non-hydrogen atom spatial position data, called after ionized.pdb makes the structure that contains hydrogen atom and hydrogen bonding parameter with this system simultaneously, called after ionized.psf;
(3) utilize NAMD_2.6_Linux-i686 software, adopt the Charmm27 field of force, with Steepest Descent method, under periodic boundary condition above-mentioned peptide-salt solusion system being carried out T.T. length is that the energy minimization of 20 psecs is handled, per 2 femtoseconds calculating is the centre of sphere with each atom once in this process, radius is the Van der Waals force of other interior this atom of atom pair of the diameter of Spherical Volume of 10 , it is the centre of sphere with each atom once that per 4 femtoseconds calculate, radius is the electric field force of other interior this atom of atom pair of the diameter of Spherical Volume of 12 , after finishing, calculating obtains the movement locus of each atom, called after minimize.dcd;
(4) then, fixing all atoms in the peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the time of using Langevin dynamics temperature control method to heat 20 psecs, system heats up gradually and is stabilized to 280-320K as a result, obtain the movement locus of each atom in this process, called after heat.dcd;
(5) use 100kcal/mol successively
2, 50kcal/mol
2, 20kcal/mol
2With 10kcal/mol
2Harmonious effect of contraction retrain above-mentioned peptide chain, adopt with (3) in the identical field of force, periodic boundary condition, Van der Waals force and electric field force computing method, use Langevin dynamics temperature control method and Nose-Hoover Langevin piston pressure control method that temperature is controlled at 300K, pressure is controlled at 1atm, difference equilibrium system 20 psecs, obtain the movement locus of all atoms in each step successively respectively, distinguish called after equ100.dcd, equ50.dcd, equ20.dcd and equ10.dcd successively;
(6) harmony to peptide chain retrains in the removal (5), adopt the field of force, periodic boundary condition, Van der Waals force and electric field force computing method, the temperature-control pressure-control method identical with (5), the PME grid length of side is set to 1 ± 0.1 , utilize PME long-range electric field force computing method, all hydrogen-oxygen bond distance in the fixed system, whole system is carried out the molecular dynamics simulations of 2 nanoseconds, obtain the movement locus of each atom in this process, called after simulate.dcd;
(7) result of calculation minimize.dcd, heat.dcd, equ100.dcd, equ50.dcd, equ20.dcd, equ10.dcd and simulate.dcd in above-mentioned (3)-(6) are written into the movement locus of all atoms of VMD-1.8.5 software observes;
(8) the conformation change process by above-mentioned movement locus analysing protein;
(9) find out the amino acid residue that plays a crucial role in the protein conformation change procedure.
2. the method for utilizing the computer simulation protein interaction as claimed in claim 1 is characterized in that: the system equilibrium temperature described in the step (4) is 310K.
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| Publication number | Priority date | Publication date | Assignee | Title |
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| CN102446235A (en) * | 2010-10-11 | 2012-05-09 | 中国石油化工股份有限公司 | Method for simulating and calculating interaction parameters among chemical components by using computer |
| CN105893759A (en) * | 2016-04-01 | 2016-08-24 | 南京大学 | Thyroid hormone disruptor virtual screening and interference activity quantitative calculating method based on nuclear receptor coregulator |
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| CN102446235A (en) * | 2010-10-11 | 2012-05-09 | 中国石油化工股份有限公司 | Method for simulating and calculating interaction parameters among chemical components by using computer |
| CN105893759A (en) * | 2016-04-01 | 2016-08-24 | 南京大学 | Thyroid hormone disruptor virtual screening and interference activity quantitative calculating method based on nuclear receptor coregulator |
| CN105893759B (en) * | 2016-04-01 | 2018-08-24 | 南京大学 | A kind of thyroid hormone replacement therapy virtual screening and its active quantitative calculation method of interference being total to regulatory factor based on nuclear receptor |
| CN107729717A (en) * | 2017-11-03 | 2018-02-23 | 四川大学 | A kind of method that computer simulation obtains g protein coupled receptor intermediate structure |
| CN107729717B (en) * | 2017-11-03 | 2019-09-27 | 四川大学 | A kind of method that computer simulation obtains g protein coupled receptor intermediate structure |
| CN109994150A (en) * | 2019-03-12 | 2019-07-09 | 华东师范大学 | A kind of dominant method for indicating albumen pocket surface layer atom and ligand interaction satisfaction degree |
| CN112116948A (en) * | 2020-09-25 | 2020-12-22 | 山东大学 | Simulation analysis method of DNA polyhedron with special branch number |
| CN113009828A (en) * | 2021-02-23 | 2021-06-22 | 桂林电子科技大学 | Anti-interference calibration method for dynamic parameters of complex mechanical system |
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