ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility

Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms probe different approaches to include protein flexibility. Here we describe a new method for docking small molecules into protein binding sites employing a Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. The energy function comprises van der Waals (VDW) interactions, an implicit solvation model, an explicit orientation hydrogen bonding potential, and an electrostatics model. In an evaluation of the scoring function the computed energy correlated with experimental small molecule binding energy with a correlation coefficient of 0.63 across a diverse set of 229 protein- small molecule complexes. The docking method produced lowest energy models with a root mean square deviation (RMSD) smaller than 2 A in 71 out of 100 protein-small molecule crystal structure complexes (self-docking). In cross-docking calculations in which both protein side-chain and small molecule internal degrees of freedom were varied the lowest energy predictions had RMSDs less than 2 A in 14 of 20 test cases.     

Protein Structure Prediction with a Combined Solvation Free Energy-Molecular Mechanics Force Field

Abstract

Models of protein structure are frequently used to determine the physical characteristics of a protein when the crystal structure is not available. We developed a procedure to optimize such models, by use of a combined solvation free energy and molecular mechanics force field. Appropriately chosen atomic solvation parameters were defined using the criterion that the resulting protein model should deviate least from the crystal structure upon a forty picosecond molecular dynamics simulation carried out using the combined force field. Several tests were performed to refine the set of atomic solvation parameters which best complement the molecular mechanics forces. Four sets of parameters from the literature were tested and an empirically optimized set is proposed. The parameters are defined on a well characterized small molecule (alanyl dipeptide) and on the highly refined crystal structure of rat trypsin, and then tested on a second highly refined crystal structure of α-lytic protease. The new set of atomic solvation parameters provides a significant improvement over molecular mechanics alone in energy minimization of protein structures. This combined force field also has advantages over the use of explicit solvent as it is possible to take solvent effects into account during energetic conformational searching when modeling a homologous protein structure from a known crystal structure.     

Divergence of evolutionary ways among common sym genes: CASTOR and CCaMK show functional conservation between two symbiosis systems and constitute the root of a common signaling pathway

In recent years a number of legume genes involved in root nodule (RN) symbiosis have been identified in the model legumes, Lotus japonicus (Lotus) and Medicago truncatula. Among them, a distinct set of genes has been categorized as a common symbiosis pathway (CSP), because they are also essential for another mutual interaction, the arbuscular mycorrhiza (AM) symbiosis, which is evolutionarily older than the RN symbiosis and is widely distributed in the plant kingdom. Based on the concept that the legume RN symbiosis has evolved from the ancient AM symbiosis, one issue is whether the CSP is functionally conserved between non-nodulating plants, such as rice, and nodulating legumes. We identified three rice CSP gene orthologs, OsCASTOR, OsPOLLUX and OsCCaMK, and demonstrated the indispensable roles of OsPOLLUX and OsCCaMK in rice AM symbiosis. Interestingly, molecular transfection of either OsCASTOR or OsCCaMK could fully complement symbiosis defects in the corresponding Lotus mutant lines for both the AM and RN symbioses. Our results not only provide a conserved genetic basis for the AM symbiosis between rice and Lotus, but also indicate that the core of the CSP has been well conserved during the evolution of RN symbiosis. Through evolution, CASTOR and CCaMK have remained as the molecular basis for the maintenance of CSP functions in the two symbiosis systems.     

A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability

A molecular mechanics model, previously validated in applications to structure prediction, is shown to reproduce experiment in predictions of protein ionization state, and in predictions of sequence and pH dependence of protein stability. Over a large dataset, 1876 values of ΔΔG of folding, the RMSD is 1.34 kcal/mol. Using an alternative measure of accuracy, either the sign of the calculated ΔΔG agrees with experiment or the absolute value of the deviation is less than 1.0 kcal/mol, 1660 of 1876 data points (88.5%) pass the condition. Relative to models used previously in computer‐aided protein design, the concept, we propose, most responsible for the performance of our model, and for the extensibility to non‐neutral values of pH, is the treatment of electrostatic energy. The electronic structure of the protein is modeled using distributed atomic multipoles. The structured liquid state of the solvent is modeled using a dielectric continuum. A modification to the energetics of the reaction field, induced by the protein in the dielectric continuum, attempts to account for preformed multipoles of solvent water molecules and ions. An adjustable weight (with optimal value.141) applied to the total vacuum energy accounts implicitly for electronic polarization. A threshold distance, beyond which pairwise atomic interactions are neglected, is not used. In searches through subspaces of sequences and conformations, efficiency remains acceptable for useful applications. Proteins 2014; 82:2497–2511. © 2014 Wiley Periodicals, Inc.     

Molecular Dynamics of the Ha-ras Protein: Nucleotide Atom-Centred Charges within the AMBER Force Field

Molecular dynamics simulations have become an essential tool for the study of biological systems. The Ha-ras protein, is a system suitable for such studies. Despite much recent progress, it is still not known exactly how the protein functions in the cell growth cycle. In this work atom-centred point charges for the guanosine nucleotide ligands are calculated and tested. To be compatible with the other AMBER force field parameters these are fitted to a molecular electrostatic potential derived from an ab initio wavefunction. The smallest basis set able to produce a stable wavefunction for the negatively charged GDP and GTP molecule ions was 3-21G* with diffuse functions added on the phosphate groups. To maintain force field integrity these charges were scaled to be equivalent to STO-3G derived values. This procedure is seen to produce a good magnesium-phosphate interaction potential when compared to 6-31++G* ab initio calculations. With the nucleotides fixed in the binding site conformation, it was found essential to include the electrostatics of the binding site in the calculation of the charges. It was also found to be inappropriate to divide the nucleotide into constituent parts for the calculations. From the calculated charges and experimental data, the nucleotide protonation states in the protein are deduced. It is unlikely that GDP is protonated, GTP probably binds one proton. The charges were tested in MD simulations of a protein modelled on the crystal structure of Tong et al., during which the dynamics of the nucleotide and binding site residues were in good agreement with the crystal structure data. The model is seen to be sensitive, not only to the inclusion of explicit solvent, but to the number of waters ligating the magnesium ion and the conformation of the loop between residues 60 and 66; both pieces of information are lacking in the crystal structure data.     

Oscillations of a molecular dusty-plasma crystal

The phonon spectra of a two-layer plasma crystal are analyzed. A simple model describing nonreciprocal forces acting between dust grains is formulated. General trends in the dynamics of a single dust molecule consisting of two vertically aligned grains are described. An integral of motion analogous to energy is found in the harmonic approximation. The conditions allowing the existence of a molecular crystal for which interaction between pairs of grains weakly affects the state of an individual molecule are determined. The oscillation spectra are obtained in an explicit form.     

Prediction of the binding energy for small molecules,peptides and proteins

A fast and reliable evaluation of the binding energy from a single conformation of a molecular complex is an important practical task. Knowledge‐based scoring schemes may not be sufficiently general and transferable, while molecular dynamics or Monte Carlo calculations with explicit solvent are too computationally expensive for many applications. Recently, several empirical schemes using finite difference Poisson–Boltzmann electrostatics to predict energies for particular types of complexes were proposed. Here, an improved empirical binding energy function has been derived and validated on three different types of complexes: protein–small ligand, protein–peptide and protein–protein. The function uses the boundary element algorithm to evaluate the electrostatic solvation energy. We show that a single set of parameters can predict the relative binding energies of the heterogeneous validation set of complexes with 2.5 kcal/mol accuracy. We also demonstrate that global optimization of the ligand and of the flexible side‐chains of the receptor improves the accuracy of the evaluation. Copyright © 1999 John Wiley & Sons, Ltd.     

Calculations on crystal packing of a flexible molecule, Leu-enkephalin

Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energetically stable packings found. The conformations of the enkephalin molecules in the crystal are not the most stable for an isolated molecule; i.e. intermolecular interactions force the isolated molecule to change conformation in order to achieve a small packing volume and an optimal packing energy in the crystal. It is found that the packing energy of an enkephalin molecule is a reasonably smooth function of its molecular volume in the unit cell, if structures with intermolecular hydrogen bonding are excluded, and is substantially independent of other details of the molecular conformation or of the crystal packing. Hydrogen bonding provides additional stabilization of the crystal structure, and would likely permit crystallization of the system if it is sufficiently dense. Solvent molecules further stabilize the structure when they can also provide intermolecular hydrogen bonds.     

Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind

Protein–protein interactions are a fundamental aspect of many biological processes. The advent of recombinant protein and computational techniques has allowed for the rational design of proteins with novel binding capabilities. It is therefore desirable to predict which designed proteins are capable of binding in vitro. To this end, we have developed a learned classification model that combines energetic and non‐energetic features. Our feature set is adapted from specialized potentials for aromatic interactions, hydrogen bonds, electrostatics, shape, and desolvation. A binding model built on these features was initially developed for CAPRI Round 21, achieving top results in the independent assessment. Here, we present a more thoroughly trained and validated model, and compare various support‐vector machine kernels. The Gaussian kernel model classified both high‐resolution complexes and designed nonbinders with 79–86% accuracy on independent test data. We also observe that multiple physical potentials for dielectric‐dependent electrostatics and hydrogen bonding contribute to the enhanced predictive accuracy, suggesting that their combined information is much greater than that of any single energetics model. We also study the change in predictive performance as the model features or training data are varied, observing unusual patterns of prediction in designed interfaces as compared with other data types. Proteins 2013; 81:1919–1930. © 2013 Wiley Periodicals, Inc.     

Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules

We recently developed a polarizable atomic multipole refinement method assisted by the AMOEBA force field for macromolecular crystallography. Compared to standard refinement procedures, the method uses a more rigorous treatment of x-ray scattering and electrostatics that can significantly improve the resultant information contained in an atomic model. We applied this method to high-resolution lysozyme and trypsin data sets, and validated its utility for precisely describing biomolecular electron density, as indicated by a 0.4-0.6% decrease in the R- and R_free-values, and a corresponding decrease in the relative energy of 0.4-0.8 Kcal/mol/residue. The re-refinements illustrate the ability of force-field electrostatics to orient water networks and catalytically relevant hydrogens, which can be used to make predictions regarding active site function, activity, and protein-ligand interaction energies. Re-refinement of a DNA crystal structure generates the zigzag spine pattern of hydrogen bonding in the minor groove without manual intervention. The polarizable atomic multipole electrostatics model implemented in the AMOEBA force field is applicable and informative for crystal structures solved at any resolution.     

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

A continuum electrostatics approach for molecular dynamics (MD) simulations of macromolecules is presented and analyzed for its performance on a peptide and a globular protein. The approach incorporates the screened Coulomb potential (SCP) continuum model of electrostatics, which was reported earlier. The model was validated in a broad set of tests some of which were based on Monte Carlo simulations that included single amino acids, peptides, and proteins. The implementation for large-scale MD simulations presented in this article is based on a pairwise potential that makes the electrostatic model suitable for fast analytical calculation of forces. To assess the suitability of the approach, a preliminary validation is conducted, which consists of (i) a 3-ns MD simulation of the immunoglobulin-binding domain of streptococcal protein G, a 56-residue globular protein and (ii) a 3-ns simulation of Dynorphin, a biological peptide of 17 amino acids. In both cases, the results are compared with those obtained from MD simulations using explicit water (EW) molecules in an all-atom representation. The initial structure of Dynorphin was assumed to be an alpha-helix between residues 1 and 9 as suggested from NMR measurements in micelles. The results obtained in the MD simulations show that the helical structure collapses early in the simulation, a behavior observed in the EW simulation and consistent with spectroscopic data that suggest that the peptide may adopt mainly an extended conformation in water. The dynamics of protein G calculated with the SCP implicit solvent model (SCP-ISM) reveals a stable structure that conserves all the elements of secondary structure throughout the entire simulation time. The average structures calculated from the trajectories with the implicit and explicit solvent models had a cRMSD of 1.1 A, whereas each average structure had a cRMSD of about 0.8A with respect to the X-ray structure. The main conformational differences of the average structures with respect to the crystal structure occur in the loop involving residues 8-14. Despite the overall similarity of the simulated dynamics with EW and SCP models, fluctuations of side-chains are larger when the implicit solvent is used, especially in solvent exposed side-chains. The MD simulation of Dynorphin was extended to 40 ns to study its behavior in an aqueous environment. This long simulation showed that the peptide has a tendency to form an alpha-helical structure in water, but the stabilization free energy is too weak, resulting in frequent interconversions between random and helical conformations during the simulation time. The results reported here suggest that the SCP implicit solvent model is adequate to describe electrostatic effects in MD simulation of both peptides and proteins using the same set of parameters. It is suggested that the present approach could form the basis for the development of a reliable and general continuum approach for use in molecular biology, and directions are outlined for attaining this long-term goal.     

Higher order organization of human placental aromatase

Aromatase (CYP19A1) is an integral membrane enzyme that catalyzes the removal of the 19-methyl group and aromatization of the A-ring of androgens. All human estrogens are synthesized from their androgenic precursors by this unique cytochrome P450. The crystal structure of active aromatase purified from human placenta has recently been determined in complex with its natural substrate androstenedione in the high-spin ferric state of heme. Hydrogen bond forming interactions and tight packing hydrophobic side chains closely complement puckering of the steroid backbone, thereby providing the molecular basis for the androgenic specificity of aromatase. In the crystal, aromatase molecules are linked by a head-to-tail intermolecular interaction via a surface loop between helix D and helix E of one aromatase molecule that penetrates the heme-proximal cavity of the neighboring, crystallographically related molecule, thus forming in tandem a polymeric aromatase chain. This intermolecular interaction is similar to the aromatase-cytochrome P450 reductase coupling and is driven by electrostatics between the negative potential surface of the D-E loop region and the positively charged heme-proximal cavity. This loop-to-proximal site link in aromatase is rather unique—there are only a few of examples of somewhat similar intermolecular interactions in the entire P450 structure database. Furthermore, the amino acids involved in the intermolecular contact appear to be specific for aromatase. Higher order organization of aromatase monomers may have implications in lipid integration and catalysis.     

The ELBA force field for coarse-grain modeling of lipid membranes

A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r) = 1). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.     

Visual methods from atoms to cells

Illustrations of molecular models are widely used for the study and dissemination of molecular structure and function. Several metaphors are commonly used to create these illustrations, and each captures a relevant aspect of the molecule and omits other aspects. Effective tools are available for rendering atomic structures by using several standard representations, and the research community is highly sophisticated in their use. Molecular properties, such as electrostatics, and large complex molecular and cellular systems currently pose challenges for representation.     

Orientation of double-helical segments in crystals of yeast phenylalanine transfer RNA

A search of the X-ray intensities of the P2₁ crystal form of yeast transfer RNA^Phe has revealed the orientation of the double-helical segments in the crystal. Because of the ambiguity imposed by the crystal symmetry on choosing the helices belonging to the same molecule, and because of the difficulty of determining lengths and positions of helices, a unique model cannot be deduced, but only a small number of types are possible. Among the possibilities are a “boot”-shaped molecule, which may be derived from an earlier model proposed by the author, by bending out the anticodon arm, and also an L-shaped molecule. The latter is, however, not oriented in the way proposed by Kim et al. (1973) for the case of the closely related orthorhombic crystal form.     

FragIt: A Tool to Prepare Input Files for Fragment Based Quantum Chemical Calculations

Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available to support these methods and help to set up reasonable input files which will lower the barrier of entry for usage by non-experts. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files. We present a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. FragIt uses the SMARTS language to locate chemically appropriate fragments in large structures and is applicable to fragmentation of any molecular system given suitable SMARTS patterns. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to prepare input files for the Fragment Molecular Orbital method in the GAMESS program package, but can be extended to other computational methods easily.     

Exploring protein native states and large-scale conformational changes with a modified generalized born model

Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as protein folding. In contrast to an earlier GB model (implemented in the AMBER-6 program), the improved version does not overstabilize the native structures relative to the finite-difference Poisson-Boltzmann continuum treatment. In addition to improving the energy balance between folded and unfolded conformers, the algorithm (available in the AMBER-7 and NAB molecular modeling packages) is shown to perform well in more than 50 ns of native-state molecular dynamics (MD) simulations of thioredoxin, protein-A, and ubiquitin, as well as in a simulation of Barnase/Barstar complex formation. For thioredoxin, various combinations of input parameters have been explored, such as the underlying gas-phase force fields and the atomic radii. The best performance is achieved with a previously proposed modification to the torsional potential in the Amber ff99 force field, which yields stable native trajectories for all of the tested proteins, with backbone root-mean-square deviations from the native structures being approximately 1.5 A after 6 ns of simulation time. The structure of Barnase/Barstar complex is regenerated, starting from an unbound state, to within 1.9 A relative to the crystal structure of the complex.     

沉淀剂类型对蛋白质晶体分子堆积的影响

以不对称单位只有一个分子的牛胰核糖核酸酶和T4溶菌酶晶体为材料,着重研究了无机盐、有机溶剂和PEG三类不同的沉淀剂对晶体分子堆积的影响,经研究发现两种蛋白质中用无机盐做沉淀剂的晶型几乎都含有面积较大的二次轴对称接触面和较少的相邻分子数,同时其含有的参与接触的非极性残基集中分布于二次轴对称接触面,而盐键则在二次轴对称接触面上分布稀少。用有机溶剂作沉淀剂的晶型却含有面积较小的非二次轴对称接触面和较多的相含分子数,而参与接触的非极性残基和直键在各个非二次轴对称接触面上随机分布,用PEG作沉淀剂的晶型其分子堆积特征总体上类似于用有机溶剂作沉淀剂的晶型,但个别晶型具有与用无机盐做沉淀剂的晶型相似的分子堆积特征,以上结果提示,用三类沉淀剂得到的不同的分子堆积特征可能与三类沉淀剂不同的诱导结晶机理密切相关。     

A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor

The Ca(2+)-dependent cysteine protease calpain along with its endogenous inhibitor calpastatin is widely distributed. The interactions between calpain and calpastatin have been studied to better understand the nature of calpain inhibition by calpastatin, which can aid the design of small molecule inhibitors to calpain. Here we present the crystal structure of a complex between a calpastatin peptide and the calcium-binding domain VI of calpain. DIC19 is a 19 residue peptide, which corresponds to one of the three interacting domains of calpastatin, which is known to interact with domain VI of calpain. We present two crystal structures of DIC19 bound to domain VI of calpain, determined by molecular replacement methods to 2.5A and 2.2A resolution. In the process of crystallizing the inhibitor complex, a new native crystal form was identified which had the homodimer 2-fold axis along a crystallographic axis as opposed to the previously observed dimer in the asymmetric unit. The crystal structures of the native domain VI and its inhibitor PD150606 (3-(4-iodophenyl)-2-mercapto-(Z)-2-propenoic acid) complex were determined with the help of molecular replacement methods to 2.0A and 2.3A resolution, respectively. In addition, we built a homology model for the complex between domain IV and DIA19 peptide of calpastatin. Finally, we present a model for the calpastatin-inhibited calpain.     

A network pharmacology‐based approach to explore the effects of Chaihu Shugan powder on a non‐alcoholic fatty liver rat model through nuclear receptors

The pathogenesis of non‐alcoholic fatty liver disease (NAFLD) is still not fully understood, and currently, no effective pharmacotherapy is available. Nuclear receptors (NRs) are important biological participants in NAFLD that exhibit great therapeutic potential. Chaihu Shugan powder (CSP) is a traditional Chinese medicine (TCM) formula that has a wide therapeutic spectrum including NAFLD, but the effective components and functional mechanisms of CSP are unclear. We adopted a network pharmacology approach using multiple databases for Gene Ontology (GO) enrichment analysis and the molecular complex detection (MCODE) method for a protein‐protein interaction (PPI) analysis, and we used molecular docking method to screen the NR targets and determine the corresponding CSP components. The screening results were validated through a NAFLD rat model that was used to explain the possible relationship between CSP and NAFLD. Finally, we screened PPARγ, FXR, PPARα, RARα and PPARδ as target genes and quercetin, kaempferol, naringenin, isorhamnetin and nobiletin as target compounds. The five components were detected through high‐performance liquid chromatography‐mass spectrometry (HPLC‐MS), the results of which aligned with the docking experiments of PPARγ, PPARα and PPARδ. After CSP intervention, the NAFLD rat model showed ameliorated effects in terms of bodyweight, hepatic histopathology, and serum and liver lipids, and the mRNA levels of PPARγ, FXR, PPARα and RARα were significantly changed. The results from this study indicate that CSP exhibits healing effects in an NAFLD model and that the network pharmacology approach to screening NR targets and determining the corresponding CSP components is a practical strategy for explaining the mechanism by which CSP ameliorates NAFLD.