Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

Comparison of simple potential functions for simulating liquid water

Introduction Statistical mechanics Molecular dynamics Monte Carlo methods Some tricks of the trade How to analyse the results Advanced simulation techniques Non-equilibrium molecular dynamics Brownian dynamics Quantum simulations Some applications Appendix A: Computers and computer simulation Appendix B: Reduced units Appendix C: Calculation of forces and torques Appendix D: Fourier transforms Appendix E: The gear predictor - corrector Appendix F: Programs on microfiche Appendix G: Random numbers References Index.

Computer Simulation of Liquids

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Flow Birefringence in Solutions of Macromolecules.

The multibody terms pertaining to the correlation between backbone−local and backbone−electrostatic interactions in the UNRES force field for energy-based protein-structure prediction, developed in...

Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

Interactions in aqueous solution

The main features of the four-alpha-helix bundle, one of the characteristic structural elements of many proteins, can be explained in terms of noncovalent interactions between the constituent helices. Conformational energy computations have been carried out on four types of four-alpha-helix bundles, each consisting of four CH3CO-(L-Ala)10-NHCH3 polypeptide chains, with various combinations of parallel and antiparallel orientations of the helices. In the bundle with the most favorable energy, all pairs of neighboring helices are oriented antiparallel--i.e., in the orientation that is favored by electrostatic interactions between the helices. In this structure, the orientation angle between neighboring helix axes is -168 degrees, within +/- 7 degrees, in close agreement with the orientation angles observed in proteins and with the value that we computed earlier for the most favorable packing of pairs of interacting alpha-helices. This orientation corresponds to a left-handed twisting of the helical bundle. The preferred handedness of this twisting arises as a result of favorable nonbonded interactions between the alpha-helices.

https://www.pnas.org/content/pnas/85/12/4295.full.pdf

Energetics of the structure of the four-alpha-helix bundle in proteins

The regeneration of bovine pancreatic ribonuclease A (RNase A) from the reduced to the native form with mixtures of oxidized and reduced dithiothreitol has been studied at 25 degrees C, pH 8.0, by using a variety of current experimental techniques, including quenching the regeneration reaction with 2-aminoethyl methanethiosulfonate, fractionation of intermediates by HPLC, and analysis by both UV and disulfide-specific detection systems. The disulfide-containing protein intermediates achieve a steady-state distribution after which the native protein regenerates at a rate comparable to the rates observed previously during the regeneration of RNase A with glutathione. Equilibrium constants at 25 degrees C, pH 8.0, for the interconversion of species containing different numbers of disulfide bonds are evaluated from the concentrations in the steady-state distribution. These equilibrium constants are compared with those obtained earlier when native RNase A is regenerated with glutathione. The observed equilibrium constants (with the dithiothreitol system) for the interconversions among all intermediates are very similar once statistical factors arising from the different numbers of disulfide-containing species in each grouping are taken into account. None of the disulfide-containing intermediates has any significant enzymatic activity, in agreement with earlier conclusions that these intermediates are considerably disordered. This is in sharp contrast to disulfide-containing intermediates populated during the regeneration of bovine pancreatic trypsin inhibitor, which have significant nativelike structure.

Regeneration of bovine pancreatic ribonuclease A. 1. Steady-state distribution.

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