Electrostatically-driven association of proteins is important to many biological functions, and understanding which amino acid residues contribute to these interactions is crucial to protein design. Theoretical calculations that are used to elucidate the role of electrostatics in association are typically based on a single experimentally determined protein structure, while an underlying rigid-body assumption is adopted. The goal of this study was to investigate the role of conformational fluctuations on electrostatic interaction energies, as applied to the electrostatic analysis of barnase-barstar. For our calculations, we apply theoretical alanine-scan mutagenesis to introduce charge perturbations by replacing every ionizable residue with alanine, one at a time. Electrostatic clustering and free energy calculations based on the Poisson-Boltzmann method are used to evaluate the effects of each perturbation. Molecular dynamics simulations are performed for the barnase-barstar parent complex and seven experimental alanine mutations from the literature, in order to introduce relaxation before and after mutation. We discuss the effects of dynamics, in the form of pre- and post-mutation relaxation, on electrostatic clustering and free energies of association in light of experimental data. We also examine the utility of nine electrostatic similarity methods for clustering of barnase alanine-scan mutants. Our calculations suggest that the rigid-body assumption is reasonable for electrostatic calculations of barnase-barstar. 相似文献
Polymers conjugated to the exterior of a protein mediate its interactions with surroundings, enhance its processability and can be used to direct its macroscopic assemblies. Most studies to date have focused on peptide–polymer conjugates based on hydrophilic polymers. Engineering amphiphilicity into protein motifs by covalently linking hydrophobic polymers has the potential to interface peptides and proteins with synthetic polymers, organic solvents, and lipids to fabricate functional hybrid materials. Here, we synthesized amphiphilic peptide–polymer conjugates in which a hydrophobic polymer is conjugated to the exterior of a heme‐binding four‐helix bundle and systematically investigated the effects of the hydrophobicity of the conjugated polymer on the peptide structure and the integrity of the heme‐binding pocket. In aqueous solution with surfactants present, the side‐conjugated hydrophobic polymers unfold peptides and may induce an α‐helix to β‐sheet conformational transition. These effects decrease as the polymer becomes less hydrophobic and directly correlate with the polymer hydrophobicity. Upon adding organic solvent to solubilize the hydrophobic polymers, however, the deleterious effects of hydrophobic polymers on the peptide structures can be eliminated. Present studies demonstrate that protein structure is sensitive to the local environment. It is feasible to dissolve amphiphilic peptide–polymer conjugates in organic solvents to enhance their solution processability while maintaining the protein structures.
The problem of approximating m data points (xi, yi) in , with a quadratic function q(x, p) with s parameters, m ≥ s, is considered. The parameter vector is to be determined so as to satisfy three conditions: (1) q(x, p) must underestimate all m data points, i.e. q(xi, p) ≤ yi, i=1,...,m. (2) The error of the approximation is to be minimized in the L1 norm. (3) The eigenvalues of H are to satisfy specified lower and upper bounds, where H is the Hessian of q(x, p) with respect to x. This is called the Quadratic Underestimator with Bounds on Eigenvalues (QUBE) problem. An algorithm for its solution (QUBE algorithm) is given and justified, and computational results presented. The QUBE algorithm has application to finding the global minimum of a basin (or funnel) shaped function with a large number of local minima. Such problems arise in computational biology where it is desired to find the global minimum of an energy surface, in order to predict native protein-ligand docking geometry (drug design) or protein structure. Computational results for a simulated docking energy surface, with n=15, are presented. It is shown that specifying a small condition number for H improves the ability of the underestimator to correctly predict the global minimum point. 相似文献
Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein–protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein–protein interaction data for any species and even other biological networks. 相似文献
The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels and (ii) the detection of the transmembrane region of a beta-barrel transmembrane protein. The geometric modelling algorithm combines a non-linear least square minimization method and a genetic algorithm in order to find the characteristics (axis, radius) of a shape with axial symmetry which best models a beta-barrel. The transmembrane region is detected by profiling the external residues of the beta-barrel along its axis in terms of hydrophobicity and existence of aromatic and charged residues. TbB-Tool implements these algorithms and is available in . A non-redundant set of 22 OMPs is used in order to evaluate the algorithms implemented and the results are very satisfying. In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results. 相似文献
Proteins are highly complex biopolymers, exhibiting a substantial degree of structural variability in their properly folded, native state. In the presence of denaturants, this heterogeneity is greatly enhanced, and fluctuations take place among vast numbers of folded and unfolded conformations via many different pathways. To better understand protein folding it is necessary to explore the structural and energetic properties of the folded and unfolded polypeptide chain, as well as the trajectories along which the chain navigates through its multi-dimensional conformational energy landscape. In recent years, single-molecule fluorescence spectroscopy has been established as a powerful tool in this research area, as it allows one to monitor the structure and dynamics of individual polypeptide chains in real time with atomic scale resolution using F?rster resonance energy transfer (FRET). Consequently, time trajectories of folding transitions can be directly observed, including transient intermediates that may exist along these pathways. Here we illustrate the power of single-molecule fluorescence with our recent work on the structure and dynamics of the small enzyme RNase H in the presence of the chemical denaturant guanidinium chloride (GdmCl). For FRET analysis, a pair of fluorescent dyes was attached to the enzyme at specific locations. In order to observe conformational changes of individual protein molecules for up to several hundred seconds, the proteins were immobilized on nanostructured, polymer coated glass surfaces specially developed to have negligible interactions with folded and unfolded proteins. The single-molecule FRET analysis gave insight into structural changes of the unfolded polypeptide chain in response to varying the denaturant concentration, and the time traces revealed stepwise transitions in the FRET levels, reflecting conformational dynamics. Barriers in the free energy landscape of RNase H were estimated from the kinetics of the transitions. 相似文献