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

The Non-clotting Component of the Human Plasma Fraction I-1 (“Cold Insoluble Globulin”)1

The conformation of angiotensin ii in aqueous solution.

The regeneration of bovine pancreatic ribonuclease A (RNase A) from the reduced to the native form with mixtures of oxidized and reduced dithiothreitol at 25 °C, pH 8.0, proceeds through two separate pathways in which separate nativelike three-disulfide species are populated. The populations of these two three-disulfide species during the regeneration process have been monitored directly through the use of a reduction pulse. A detailed kinetic analysis of the regeneration process using improved experimental procedures and data analysis has been carried out to obtain rate constants for disulfide interconversion among the various disulfide-bonded intermediates. This analysis indicates that these two pathways can account for essentially 100% of the native protein regenerated and that the relative amount of native protein regenerated through these two pathways is insensitive to the redox conditions used. These results indicate that the rate-determining step in both pathways involves formation of the nativelik...

Regeneration of bovine pancreatic ribonuclease A: detailed kinetic analysis of two independent folding pathways.

Bovine pancreative ribonuclease A (RNase A), denatured by 3.5 M LiClO4 (pH 3.0), has some ordered conformation as indicated by a high retention of alpha-helix and compact structure. This effect of LiClO4 was confirmed by the observation that the alpha-helix of isolated S-peptide is stabilized in the presence of 3.5 M LiClO4 (pH 3.0), as measured by circular dichroism and nuclear magnetic resonance. The effect of the retained alpha-helices and compact structure on the folding kinetics of RNase A was studied by comparison with the kinetic folding from urea-denatured RNase A, which has no ordered structure. In contrast to our previous study under folding conditions [Denton, J.B., Konishi, Y., & Scheraga, H. A. (1982) Biochemistry 21, 5155], the kinetic folding/unfolding experiments were carried out here in the transition regions between native and LiClO4-denatured RNase A and between native and urea-denatured RNase A. The measured relaxation times were extrapolated to the triple point, where native RNase A, LiClO4-denatured RNase A, and urea-denatured RNase A have the same thermodynamic stability and are at the same concentration, in order to compare the rates of these two processes under the same solvent conditions. Under these conditions, both folding and unfolding pathways are studied simultaneously without any accumulated intermediates. No significant acceleration of folding was observed from LiClO4-denatured RNase A as compared to that from urea-denatured RNase A. This indicates that all ordered structures in RNase A are not equivalent in their influence on the folding pathway; some may play an essential role and some may not.(ABSTRACT TRUNCATED AT 250 WORDS)

Folding of ribonuclease A from a partially disordered conformation. Kinetic study under folding conditions

Reduced RNase A was reoxidized, and the incorrectly formed disulfide bonds were reshuffled to the native ones by oxidized and reduced glutathiones, as described in the first paper of this series. The intermediates in the regeneration of the disulfide bonds were trapped without any chemical modification and were fractionated on a carboxymethylcellulose column at pH 3.5 with a salt gradient. The elution curves of the partially regenerated RNase A from the carboxymethylcellulose column were obtained by measurement of the absorption at 275 nm and by determination of the SH content (of cysteine residues) and consisted of 11 fractions, G8, G7, G6, G5, G4, G3, G2, G1, G0, N, and F. Some of the fractions were isolated, and their measured molecular weights were consistent with those of monomeric RNase A. Fraction F had a molecular weight between that of the monomer and dimer, so that this fraction could not be identified. The regeneration pathway could be represented in terms of two simple reactions, RNase A(-SH) + GSSG in equilibrium or formed from RNase A(-SSG) + GSH and RNase A(-SH-SSG) in equilibrium RNase A(greater than S2) + GSH, which produced 24 monomeric intermediates (not counting the fully reduced and the native species), which differed from each other in their amino acid composition. These 24 intermediates, plus the fully reduced protein, were assigned to fractions G8--G0 (as indicated in the last column of Table I), with the aid of data from amino acid analysis, SH content, and the elution position on the carboxymethylcellulose column chromatogram. Since the regeneration reaction rapidly reached a preequilibrium among the intermediates and the fully reduced RNase A prior to the rate-limiting steps, i.e., the relative concentrations of the intermediates and fully reduced RNase A became constant with reaction time, the populations of some of the intermediates in preequilibrium were estimated by curve fitting of the elution pattern from the carboxymethylcellulose column chromatogram. The equilibrium constants among the intermediates were calculated from their populations at preequilibrium. These equilibrium constants were "extrapolated" to other intermediates whose populations could not be estimated by curve fitting, and the relative populations of all of the possible intermediates at preequilibrium were thereby represented as a function of the concentrations of reduced and oxidized glutathiones. The regeneration process was also restarted from several of the isolated intermediates, and the resulting distribution of intermediates was consistent with that from which the equilibrium constants were determined, supporting the representation of the regeneration pathways in terms of two simple reactions. Thus, the equilibrium treatment of the regeneration pathways was useful to characterize the preequilibrium state, i.e., to identify the intermediates prior to the rate-limiting steps in the pathways and to estimate their stabilities at preequilibrium at various concentrations of reduced and oxidized glutathiones.

Regeneration of ribonuclease A from the reduced protein. Isolation and identification of intermediates, and equilibrium treatment.

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