Protein-protein Docking Simulations Research Articles

Development of a Scoring Method for Predicting Protein Complex Structures

The information about protein-protein interactions increases much more rapidly than the increase of the number of the tertiary structures of those protein complexes. Therefore, precise prediction of protein complex structures by protein-protein docking simulations is required. When the protein complex is rebuilt from its component protomers which derive from experimentally determined complex structure (native structure) by docking, the complex models with rmsd < 10 A from the native structure (near-native model) could be obtained, along with a great number of false positives (decoy). The separation of near-native models from many decoys is therefore needed in the prediction of complex structures by docking. In this study, we developed the method for scoring docking models so that the near-native models were higher in rank than decoys, based on the assumption that the interfaces of near-native models are more complementary in terms of surface properties and shapes compared to those of decoys.

Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme

It is known that bacteria contain inhibitors of lysozyme activity. The recently discovered Escherichia coli inhibitor of vertebrate lysozyme (Ivy) and its potential interactions with several goose-type (g-type) lysozymes from fish were studied using functional enzyme assays, comparative homology modelling, protein-protein docking, and molecular dynamics simulations. Enzyme assays carried out on salmon g-type lysozyme revealed a lack of inhibition by Ivy. Detailed analysis of the complexes formed between Ivy and both hen egg white lysozyme (HEWL) and goose egg white lysozyme (GEWL) suggests that electrostatic interactions make a dominant contribution to inhibition. Comparison of three dimensional models of aquatic g-type lysozymes revealed important insertions in the beta domain, and specific sequence substitutions yielding altered electrostatic surface properties and surface curvature at the protein-protein interface. Thus, based on structural homology models, we propose that Ivy is not effective against any of the known fish g-type lysozymes. Docking studies suggest a weaker binding mode between Ivy and GEWL compared to that with HEWL, and our models explain the mechanistic necessity for conservation of a set of residues in g-type lysozymes as a prerequisite for inhibition by Ivy.

Structural Characterization of Ca2+-ATPase-Bound Phospholamban in Lipid Bilayers by Solid-State Nuclear Magnetic Resonance (NMR) Spectroscopy,

Phospholamban (PLN) regulates cardiac contractility by modulation of sarco(endo)plasmic reticulum calcium ATPase (SERCA) activity. While PLN and SERCA1a, an isoform from skeletal muscle, have been structurally characterized in great detail, direct information about the conformation of PLN in complex with SERCA has been limited. We used solid-state NMR (ssNMR) spectroscopy to deduce structural properties of both the A 36F 41A 46 mutant (AFA-PLN) and wild-type PLN (WT-PLN) when bound to SERCA1a after reconstitution in a functional lipid bilayer environment. Chemical-shift assignments in all domains of AFA-PLN provide direct evidence for the presence of two terminal alpha helices connected by a linker region of reduced structural order that differs from previous findings on free PLN. ssNMR experiments on WT-PLN show no significant difference in binding compared to AFA-PLN and do not support the coexistence of a significantly populated dynamic state of PLN after formation of the PLN/SERCA complex. A combination of our spectroscopic data with biophysical and biochemical data using flexible protein-protein docking simulations provides a structural basis for understanding the interaction between PLN and SERCA1a.

Proposed structural models of human factor Va and prothrombinase.

The prothrombinase complex consists of factor Xa, FVa, calcium ions, and phospholipid membrane. The prothrombinase complex plays a key role in the blood coagulation process. To derive solvent-equilibrated models of human FVa and the prothrombinase complex. Several modeling techniques have been employed, including homology modeling, protein-protein docking, and molecular dynamics simulation methods, to build the structural models. We found, upon simulation, a possibly significant shift towards planarity of the five FVa domains. To estimate a prothrombinase structure, we docked an FXa model to the equilibrated FVa model using experimental data as docking filters. We found that simulation of the docked complex led to some changes in the protein-protein contacts, but not buried surface area, as compared to the initial docking model. Possible locations of prothrombin binding to prothrombinase are indicated.

Fragment Library-Based Representation System for Protein Conformation

The representation system for protein conformation has a crucial effect on the speed of various protein-related simulations, including ab initio protein structure prediction and protein-protein docking simulation. Usually, the finer a representation system, the longer is the computational time required to employ the representation system in simulations. On the other hand, very coarse lattice systems cannot be directly applied to the simulation problems with real proteins. We report a new, fragment library-based protein conformation representation system, prepared by clustering amino acid conformations from 154 proteins. This system was composed of 64 most representative fragments per each amino acid, and based on the unified residue approach in which two spheres per amino acid were used. It could represent the conformation of the 82 proteins in an independent test set with the mean and standard deviation RMSD of 1.01 and 0.09 A, respectively, based on the position of alpha carbons and the centers of mass of sidechains.

Dynamic Mechanism for the Autophosphorylation of CheA Histidine Kinase: Molecular Dynamics Simulations

The two-component system (TCS) is an important signal transduction component for most bacteria. This signaling pathway is mediated by histidine kinases via autophosphorylation between P1 and P4 domains. Taking chemotaxis protein CheA as a model of TCS, the autophosphorylation mechanism of the TCS histidine kinases has been investigated in this study by using a computational approach integrated homology modeling, ligand-protein docking, protein-protein docking, and molecular dynamics (MD) simulations. Four nanosecond-scale MD simulations were performed on the free P4 domain, P4-ATP, P4-TNPATP, and P1-P4-ATP complexes, respectively. Upon its binding to the binding pocket of P4 with a folded conformation, ATP gradually extends to an open state with help from a water molecule. Meanwhile, ATP forms two hydrogen bonds with His413 and Lys494 at this state. Because of the lower energy of the folded conformations, ATP shrinks back to its folded conformations, leading to the rupture of the hydrogen bond between ATP and Lys494. Consequently, Lys494 moves away from the pocket entrance, resulting in an open of the ATP lid of P4. It is the open state of P4 that can bind tightly to P1, where the His45 of P1 occupies a favorable position for its autophosphorylation from ATP. This indicates that ATP is not only a phosphoryl group donor but also an activator for CheA phosphorylation. Accordingly, a mechanism of the autophosphorylation of CheA is proposed as that the ATP conformational switch triggers the opening of the ATP lid of P4, leading to P1 binding tightly, and subsequently autophosphorylation from ATP to P1.

The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.

The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift perturbations for 1H and 15N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c. Protein-protein docking simulations have been performed for the binary cytochrome b5-cytochrome c and ternary (cytochrome b5)-(cytochrome c)2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b5. Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex.

Modelling and simulation: a computational perspective in anticancer drug discovery.

The availability of high-quality molecular graphics tools in the public domain is changing the way macromolecular structure is perceived by researchers, educators and students alike. Computational methods have become increasingly important in a number of areas such as comparative or homology modelling, functional site location, characterization of ligand-binding sites in proteins, docking of small molecules into protein binding sites, protein-protein docking, and molecular dynamics simulations. The results obtained yield information that sometimes is beyond current experimental possibilities and can be used to guide and improve a vast array of experiments. On the basis of our improved level of understanding of molecular recognition and the widespread availability of target structures, it is reasonable to assume that computational methods will continue aiding not only in the design and interpretation of hypothesis-driven experiments in the field of cancer research but also in the rapid generation of new hypotheses.

An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF–VIIa–Xa): a protein–protein docking and molecular dynamics refinement study

Tissue factor (TF)-bound factor (F)VIIa plays a critical role in activating FX, an event that rapidly results in blood coagulation. Despite recent advances in the structural information about soluble TF (sTF)-bound VIIa and Xa individually, the atomic details of the ternary complex are not known. As part of our long-term goal to provide a structural understanding of the extrinsic blood coagulation pathway, we built an all atom solution-equilibrated model of the human sTF-VIIa-Xa ternary complex using protein-protein docking and molecular dynamics (MD) simulations. The starting structural coordinates of sTF-VIIa and Xa were derived from dynamically equilibrated solution structures. Due to the flexible nature of the light-chain of the Xa molecule, a three-stage docking approach was employed in which SP (Arg195-Lys448)/EGF2 (Arg86-Arg139), EGF1 (Asp46-Thr85) and GLA (Ala1-Lys45) domains were docked in a sequential manner. The rigid-body docking approach of the FTDOCK method in conjunction with filtering based on biochemical knowledge from experimental site-specific mutagenesis studies provided the strategy. The best complex obtained from the docking experiments was further refined using MD simulations for 3 ns in explicit water. In addition to explaining most of the known experimental site-specific mutagenesis data pertaining to sTF-VIIa, our model also characterizes likely enzyme-binding exosites on FVIIa and Xa that may be involved in the ternary complex formation. According to the equilibrated model, the 140s loop of VIIa serves as the key recognition motif for complex formation. Stable interactions occur between the FVIIa 140s loop and the FXa -strand B2 region near the sodium-binding domain, the 160 s loop and the N-terminal activation loop regions. The helical-hydrophobic stack region that connects the GLA and EGF1 domains of VIIa and Xa appears to play a potential role in the membrane binding region of the ternary complex. The proposed model may serve as a reasonable structural basis for understanding the exosite-mediated substrate recognition of sTF-VIIa and to advance understanding of the TFPI-mediated regulatory pathway of the extrinsic blood coagulation cascade.

Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin.

The structural characterization of a complex of alpha-bungarotoxin with a recombinant antibody fragment that mimics the acetylcholine receptor was achieved using docking simulation procedures. To drive the computer simulation towards a limited set of solutions with biological significance, a filter, incorporating general considerations of antigen-antibody interactions, specificity of the selected antibody fragment and results from alpha-bungarotoxin epitope mapping, was adopted. Two similar structures were obtained for the complex, both of them stabilized by cation-pi and hydrophobic interactions due to tyrosilyl residues of the antibody fragment. Site-directed mutagenesis studies, removing each of the latter aromatic residues and causing full inactivation of the interaction process between the antibody fragment and the neurotoxin, support the validity of the calculated structure of the complex.