Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.     

源于大肠杆菌蛋白的表达、液相色谱复性与纯化新进展

对近两年来源于大肠杆菌（Escherichia coli,E．coli）的蛋白表达和用蛋白折叠液相色谱（protein folding liquid chromatography,PFLC）法对所形成的包涵体目标蛋白的复性并同时纯化的新近发展做了简要的介绍和评述．PFLC法用于包涵体蛋白分离、纯化很广,其特点是除了在色谱柱上将目标蛋白与其他组分分开,还同时要在色谱柱上进行包涵体蛋白折叠．可以说,现代生物技术中所用的大多数有价值蛋白产品的制备仍然有赖于不同机理的液相色谱（Lc）法．而用PFLC法对源于E．coli的蛋白的制备方法更具可塑性和容易达到规模化,其生成本可以成倍地降低．该文主要内容包括了E．coli蛋白的表达及样品前处理、PFLC的实用范围、PFLC的优化、PFLC中的新技术、新设备和新方法、PFLC的分子学机理、应用事例及对未来的展望．     

Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape

Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure‐based computer‐aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand–protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state‐of‐the‐art docking programs. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Molecular chaperones, folding catalysts, and the recovery of active recombinant proteins fromE. coli

The high-level expression of recombinant gene products in the gramnegative bacteriumEscherichia coli often results in the misfolding of the protein of interest and its subsequent degradation by cellular proteases or its deposition into biologically inactive aggregates known as inclusion bodies. It has recently become clear that in vivo protein folding is an energy-dependent process mediated by two classes of folding modulators. Molecular chaperones, such as the DnaK-DnaJ-GrpE and GroEL-GroES systems, suppress off-pathway aggregation reactions and facilitate proper folding through ATP-coordinated cycles of binding and release of folding intermediates. On the other hand, folding catalysts (foldases) accelerate rate-limiting steps along the protein folding pathway such as thecis/trans isomerization of peptidyl-prolyl bonds and the formation and reshuffling of disulfide bridges. Manipulating the cytoplasmic folding environment by increasing the intracellular concentration of all or specific folding modulators, or by inactivating genes encoding these proteins, holds great promise in facilitating the production and purification of heterologous proteins. Purified folding modulators and artificial systems that mimic their mode of action have also proven useful in improving the in vitro refolding yields of chemically denatured polypeptides. This review examines the usefulness and limitations of molecular chaperones and folding catalysts in both in vivo and in vitro folding processes.     

Interactions of proteins with uniform colloidal hematite and chromium hydroxide particles. II. Stability and mobility

Stability of hematite and chromium hydroxide particles covered by ovalbumin, -globulin, and lysozyme, respectively, and mobilities of the same coated particles in aqueous media were investigated as a function of the pH, ionic strenght [NaNO₃, Mg(NO₃)₂], and the amount of added proteins. It was found that ovalbumin causes electrosteric stabilization of dispersions at pH values other than 5, while flocculation occurred at pH 5 (which was the i.e.p. of the coated particles). Mobility curves of ovalbumin covered particles resembled those of the pure protein. Dispersions with -globulin flocculated at and around the i.e.p. of the macromolecule (pH7). The mobility curves of -gobulin-coated sols were intermediate between those of the protein and of the cores, and were dependent upon the amount of adsorbed -globulin. Heterocoagulation was observed for both hematite and chromium hydroxide dispersions with lysozyme. Mobilities of lysozyme covered particles were between those of the cores and of the protein, but were not dependent upon the quantity of adsorbed polymer.Supported by the NSF Grant CHE-9108420Part of a Ph.D. Thesis