Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

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

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The ferritins: molecular properties, iron storage function and cellular regulation☆

Water electrolysis is considered as the most promising technology for hydrogen production. Much research has been devoted to developing efficient electrocatalysts for hydrogen production via the hydrogen evolution reaction (HER) and oxygen production via the oxygen evolution reaction (OER). The optimum electrocatalysts can drive down the energy costs needed for water splitting via lowering the overpotential. A number of cobalt (Co)-based materials have been developed over past years as non-noble-metal heterogeneous electrocatalysts for HER and OER. Recent progress in this field is summarized here, especially highlighting several important bifunctional catalysts. Various approaches to improve or optimize the electrocatalysts are introduced. Finally, the current existing challenges and the future working directions for enhancing the performance of Co-implicated electrocatalysts are proposed.

Recent Progress in Cobalt‐Based Heterogeneous Catalysts for Electrochemical Water Splitting

Active and stable electrocatalysts made from earth-abundant elements are key to water splitting for hydrogen production through electrolysis. The growth of NiSe nanowire film on nickel foam (NiSe/NF) insitu by hydrothermal treatment of NF using NaHSe as Se source is presented. When used as a 3D oxygen evolution electrode, the NiSe/NF exhibits high activity with an overpotential of 270mV required to achieve 20mAcm(-2) and strong durability in 1.0M KOH, and the NiOOH species formed at the NiSe surface serves as the actual catalytic site. The system is also highly efficient for catalyzing the hydrogen evolution reaction in basic media. This bifunctional electrode enables a high-performance alkaline water electrolyzer with 10mAcm(-2) at a cell voltage of 1.63V.

NiSe Nanowire Film Supported on Nickel Foam: An Efficient and Stable 3D Bifunctional Electrode for Full Water Splitting

The structure of the METTL3–METTL14 complex, which mediates N6-adenosine methylation of RNA, suggests that the METTL3 subunit is the catalytic core while METTL14 serves to bind RNA. The various base modifications now known to occur in messenger RNA and long non-coding RNA are reversible, and are utilized to dynamically modify the function of the RNA. The N6-methyladenosine modification is removed by an enzyme complex comprising METTL3 and METTL14. Ping Yin and colleagues have solved structures of the methyltransferase domains of this heterodimeric complex with and without ligand. Surprisingly, the S-adenosyl methionine ligand was found only the METTL3 pocket, not in METTL14. This suggests a model in which there is a single catalytic subunit, with METTL3 functioning as an RNA binding platform. The reported structures provide unprecedented mechanistic insight into m6A RNA methylation and suggest new opportunities for the development of therapeutic agents. Chemical modifications of RNA have essential roles in a vast range of cellular processes1,2,3. N6-methyladenosine (m6A) is an abundant internal modification in messenger RNA and long non-coding RNA that can be dynamically added and removed by RNA methyltransferases (MTases) and demethylases, respectively2,3,4,5. An MTase complex comprising methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) efficiently catalyses methyl group transfer6,7. In contrast to the well-studied DNA MTase8, the exact roles of these two RNA MTases in the complex remain to be elucidated. Here we report the crystal structures of the METTL3–METTL14 heterodimer with MTase domains in the ligand-free, S-adenosyl methionine (AdoMet)-bound and S-adenosyl homocysteine (AdoHcy)-bound states, with resolutions of 1.9, 1.71 and 1.61 A, respectively. Both METTL3 and METTL14 adopt a class I MTase fold and they interact with each other via an extensive hydrogen bonding network, generating a positively charged groove. Notably, AdoMet was observed in only the METTL3 pocket and not in METTL14. Combined with biochemical analysis, these results suggest that in the m6A MTase complex, METTL3 primarily functions as the catalytic core, while METTL14 serves as an RNA-binding platform, reminiscent of the target recognition domain of DNA N6-adenine MTase9,10. This structural information provides an important framework for the functional investigation of m6A.

Structural basis of N 6 -adenosine methylation by the METTL3–METTL14 complex

Protein–protein interactions are involved in a large number of biological processes, and though X-ray crystallography and nuclear magnetic resonance spectroscopy can be used to examine two (or more) proteins in a complex, it is difficult to establish how the two proteins interact before they form this final complex. Tang et al. have used nuclear magnetic resonance spectroscopy to directly visualize an ensemble of transient, non-specific encounter complexes for the first binary complex in the bacterial phosphotransferase system (the N-terminal domain of enzyme I and the phosphocarrier protein HPr). Of particular interest is the observation that the distribution of encounter complexes correlates with the electrostatic surface potentials on the interacting proteins. Nuclear magnetic resonance spectroscopy is used to visualize directly an ensemble of transient, non-specific 'encounter' complexes for the first binary complex in the bacterial phosphotransferase system (the N-terminal domain of enzyme I and the phosphocarrier protein HPr). An atomic probability distribution map suggests that long-range electrostatic interactions facilitate the formation of the final protein–protein complex by reducing the dimensionality of the search process. Kinetic data on a number of protein–protein associations have provided evidence for the initial formation of a pre-equilibrium encounter complex that subsequently relaxes to the final stereospecific complex1. Site-directed mutagenesis2,3,4 and brownian dynamics simulations5,6,7 have suggested that the rate of association can be modulated by perturbations in charge distribution outside the direct interaction surfaces. Furthermore, rate enhancement through non-specific binding may occur by either a reduction in dimensionality8 or the presence of a short-range, non-specific attractive potential9. Here, using paramagnetic relaxation enhancement, we directly demonstrate the existence and visualize the distribution of an ensemble of transient, non-specific encounter complexes under equilibrium conditions for a relatively weak protein–protein complex between the amino-terminal domain of enzyme I and the phosphocarrier protein HPr. Neither the stereospecific complex10 alone nor any single alternative conformation can account fully for the intermolecular paramagnetic relaxation enhancement data. Restrained rigid-body simulated annealing refinement against the paramagnetic relaxation enhancement data enables us to obtain an atomic probability distribution map of the non-specific encounter complex ensemble that qualitatively correlates with the electrostatic surface potentials on the interacting proteins. Qualitatively similar results are presented for two other protein–protein complexes.

Visualization of transient encounter complexes in protein-protein association.

Large-scale domain rearrangements in proteins have long been recognized to have a critical function in ligand binding and recognition, catalysis and regulation. Crystal structures have provided a static picture of the apo (usually open) and holo usually closed) states. The general question arises as to whether the apo state exists as a single species in which the closed state is energetically inaccessible and interdomain rearrangement is induced by ligand or substrate binding, or whether the predominantly open form already coexists in rapid equilibrium with a minor closed species. The maltose-binding protein (MBP), a member of the bacterial periplasmic binding protein family, provides a model system for investigating this problem because it has been the subject of extensive studies by crystallography, NMR and other biophysical techniques. Here we show that although paramagnetic relaxation enhancement (PRE) data for the sugar-bound form are consistent with the crystal structure of holo MBP, the PRE data for the apo state are indicative of a rapidly exchanging mixture (ns to mus regime) of a predominantly ( approximately 95%) open form (represented by the apo crystal structure) and a minor (approximately 5%) partially closed species. Using ensemble simulated annealing refinement against the PRE data we are able to determine a ensemble average structure of the minor apo species and show that it is distinct from the sugar-bound state.

Open-to-Closed Transition in Apo Maltose-Binding Protein Observed by Paramagnetic NMR.

The myristoylated matrix protein (myr-MA) of HIV functions as a regulator of intracellular localization, targeting the Gag precursor polyprotein to lipid rafts in the plasma membrane during virus assembly and dissociating from the membrane during infectivity for nuclear targeting of the preintegration complex. Membrane release is triggered by proteolytic cleavage of Gag, and it has, until now, been believed that proteolysis induces a conformational change in myr-MA that sequesters the myristyl group. NMR studies reported here reveal that myr-MA adopts myr-exposed [myr(e)] and -sequestered [myr(s)] states, as anticipated. Unexpectedly, the tertiary structures of the protein in both states are very similar, with the sequestered myristyl group occupying a cavity that requires only minor conformational adjustments for insertion. In addition, myristate exposure is coupled with trimerization, with the myristyl group sequestered in the monomer and exposed in the trimer (Kassoc = 2.5 ± 0.6 × 108 M–2). The equilibrium constant is shifted ≈20-fold toward the trimeric, myristate-exposed species in a Gag-like construct that includes the capsid domain, indicating that exposure is enhanced by Gag subdomains that promote self-association. Our findings indicate that the HIV-1 myristyl switch is regulated not by mechanically induced conformational changes, as observed for other myristyl switches, but instead by entropic modulation of a preexisting equilibrium.

https://www.pnas.org/content/pnas/101/2/517.full.pdf

Chun Tang

Papers

NiSe Nanowire Film Supported on Nickel Foam: An Efficient and Stable 3D Bifunctional Electrode for Full Water Splitting

Structural basis of N 6 -adenosine methylation by the METTL3–METTL14 complex

Visualization of transient encounter complexes in protein-protein association.

Open-to-Closed Transition in Apo Maltose-Binding Protein Observed by Paramagnetic NMR.

Entropic switch regulates myristate exposure in the HIV-1 matrix protein.