Multivariate survival analysis with positive stable frailties

In this paper, we describe Bayesian modeling of dependent multivariate survival data using positive stable frailty distributions. A flexible baseline hazard formulation using a piecewise exponential model with a correlated prior process is used. The estimation of the stable law parameter together with the parameters of the (conditional) proportional hazards model is facilitated by a modified Gibbs sampling procedure. The methodology is illustrated on kidney infection data (McGilchrist and Aisbett, 1991).     

Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors

Abstract

Histone deacetylases (HDACs) are implicated in the pathology of various cancers, and their pharmacological blockade has proven to be promising in reversing the malignant phenotypes. However, lack of crystal structures of some of the human HDAC isoforms (e.g., HDAC10) hinders the design of the isoform-selective inhibitor. Here, the recently solved X-ray crystal structure of Danio rerio (zebrafish) HDAC10 (Protein Data Bank (PDB) ID; 5TD7, released on 24 May 2017) was retrieved from the PDB and used as a template structure to model the three-dimensional structure of human HDAC10. The overall quality of the best model (M0017) was assessed by computing its z-score—a measure of the deviation of the total energy of the structure with respect to an energy distribution derived from random conformations and by docking of known HDAC10 inhibitors to its catalytic cavity. Furthermore, to identify potential HDAC10-selective inhibitor ligand-based virtual screening was carried out against the ZINC database. The free modeled structure of HDAC10 and its complexes with quisinostat and the highest-ranked compound ZINC19749069 were submitted to molecular dynamics simulation. The comparative analysis of root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration (Rg), and potential energy of these systems showed that HDAC10-ZINC19749069 complex remained the most stable over time. Thus, M0017 could be potentially used for structure-based inhibitor against HDAC10, and ZINC19749069 may provide a scaffold for further optimization.

Communicated by Ramaswamy H. Sarma     

Impact of p62/SQSTM1 UBA domain mutations linked to Paget's disease of bone on ubiquitin recognition

The scaffold protein p62/SQSTM1 acts as a hub in regulating a diverse range of signaling pathways which are dependent upon a functional ubiquitin-binding C-terminal UBA domain. Mutations linked to Paget's disease of bone (PDB) commonly cluster within the UBA domain. The p62 UBA domain is unique in forming a highly stable dimer which regulates ubiquitin recognition by using overlapping surface patches in both dimerization and ubiquitin binding, making the two association events competitive. NMR structural analysis and biophysical methods show that some PDB mutations modulated the ubiquitin binding affinity by both direct and indirect mechanisms that affect UBA structural integrity, dimer stability, and contacts at the UBA-ubiquitin interface. In other cases, common PDB mutations (P392L in particular) result in no significant change in ubiquitin binding affinity for the UBA domain in isolation; however, all PDB UBA mutations lead to loss of function with respect to ubiquitin binding in the context of full-length p62, suggesting a more complex underlying mechanism.     

Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study

The fragment molecular orbital (FMO) method has enabled electronic structure calculations and geometry optimizations of very large molecules with ab initio quality. We applied the method to four FK506 binding protein (FKBP) complexes (denoted by their PDB codes 1fkb, 1fkf, 1fkg, and 1fki) containing rapamycin, FK506, and two synthetic ligands. The geometries of reduced complex models were optimized at the restricted Hartree–Fock (FMO‐RHF) level using the 3‐21G basis set, and then for a better estimate of binding, the energetics were refined at a higher level of theory (2nd order Møller–Plesset perturbation theory FMO‐MP2 with the 6‐31G* basis set). Thus, obtained binding energies were ?103.9 (?82.0), ?102.2 (?69.2), ?70.1 (?57.7), and ?71.3 (?55.3) kcal/mol for 1fkb, 1fkf, 1fkg, and 1fki, respectively, where the correlation contribution is given in parentheses. The results show that the electron correlation contribution to binding is extremely important, and it accounts for 70–80% of the binding energy. The molecular recognition mechanism of FKBP was analyzed in detail based on the FMO‐pair interactions between protein residues and the ligands. Solvation effects on the protein–ligand binding were estimated using the Poisson–Boltzmann/surface area model. Proteins 2007. © 2007 Wiley‐Liss, Inc.     

Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation

The Helmholtz free energy, F, plays an important role in proteins because of their rugged potential energy surface, which is 'decorated' with a tremendous number of local wells (denoted microstates, m). F governs protein folding, whereas differences DeltaF(mn) determine the relative populations of microstates that are visited by a flexible cyclic peptide or a flexible protein segment (e.g. a surface loop). Recently developed methodologies for calculating DeltaF(mn) (and entropy differences, DeltaS(mn)) mainly use thermodynamic integration and calculation of the absolute F; interesting new approaches in these categories are the adaptive integration method and the hypothetical scanning molecular dynamics method, respectively.     

Exploring the mechanism how AF9 recognizes and binds H3K9ac by molecular dynamics simulations and free energy calculations

Histone acetylation is a very important regulatory mechanism in gene expression in the chromatin context. A new protein family‐YEATS domains have been found as a novel histone acetylation reader, which could specific recognize the histone lysine acetylation. AF9 is an important one in the YEATS family. Focused on the AF9‐H3K9ac (K9 acetylation) complex (ALY) (PDB code: 4TMP) and a serials of mutants, MUT (the acetyllsine of H3K9ac was mutated to lysine), F59A, G77A, and D103A, we applied molecular dynamics simulation and molecular mechanics Poisson?Boltzmann (MM‐PBSA) free energy calculations to examine the role of AF9 protein in recognition interaction. The simulation results and analysis indicate that some residues of the protein have significant influence on recognition and binding to H3K9ac peptides and hydrophobic surface show the hydrophobic interactions play an important role in the binding. Our work can give important information to understand how the protein AF9 recognizes the peptides H3K9ac. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 779–786, 2016.     

Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices

Integrins are heterodimeric (αβ) cell surface receptors that are activated to a high affinity state by the formation of a complex involving the α/β integrin transmembrane helix dimer, the head domain of talin (a cytoplasmic protein that links integrins to actin), and the membrane. The talin head domain contains four sub-domains (F0, F1, F2 and F3) with a long cationic loop inserted in the F1 domain. Here, we model the binding and interactions of the complete talin head domain with a phospholipid bilayer, using multiscale molecular dynamics simulations. The role of the inserted F1 loop, which is missing from the crystal structure of the talin head, PDB:3IVF, is explored. The results show that the talin head domain binds to the membrane predominantly via cationic regions on the F2 and F3 subdomains and the F1 loop. Upon binding, the intact talin head adopts a novel V-shaped conformation which optimizes its interactions with the membrane. Simulations of the complex of talin with the integrin α/β TM helix dimer in a membrane, show how this complex promotes a rearrangement, and eventual dissociation of, the integrin α and β transmembrane helices. A model for the talin-mediated integrin activation is proposed which describes how the mutual interplay of interactions between transmembrane helices, the cytoplasmic talin protein, and the lipid bilayer promotes integrin inside-out activation.     

A modeled structure for amidase-03 from Bacillus anthracis

Homology models of amidase-03 from Bacillus anthracis were constructed using Modeller (9v2). Modeller constructs protein models using an automated approach for comparative protein structure modeling by the satisfaction of spatial restraints. A template structure of Listeria monocytogenes bacteriophage PSA endolysin PlyPSA (PDB ID: 1XOV) was selected from protein databank (PDB) using BLASTp with BLOSUM62 sequence alignment scoring matrix. We generated five models using the Modeller default routine in which initial coordinates are randomized and evaluated by pseudo-energy parameters. The protein models were validated using PROCHECK and energy minimized using the steepest descent method in GROMACS 3.2 (flexible SPC water model in cubic box of size 1 Å instead of rigid SPC model). We used G43a1 force field in GROMACS for energy calculations and the generated structure was subsequently analyzed using the VMD software for stereo-chemistry, atomic clash and misfolding. A detailed analysis of the amidase-03 model structure from Bacillus anthracis will provide insight to the molecular design of suitable inhibitors as drug candidates.     

Unravelling novel congeners from acetyllysine mimicking ligand targeting a lysine acetyltransferase PCAF bromodomain

p300/CBP Associated Factor (PCAF) bromodomain (BRD), a lysine acetyltransferases, has emerged as a promising drug target as its dysfunction is linked to onset and progression of several diseases like cancer, diabetes, AIDS, etc. In this study, a three featured E-Pharmacophore (ARR) was generated based on acetyllysine mimicking inhibitor of PCAF BRD which is available as co-crystal structure (PDB ID: 5FDZ). It was used for filtering small molecule databases followed by molecular docking and consequently validated using enrichment calculation. The resulted hits were found to be congeners which show the predictive power of E-Pharmacophore hypothesis. Further, Induced Fit Docking method, Binding energy calculation, ADME prediction, Single Point Energy calculation and Molecular Dynamics simulation were performed to find better hits against PCAF BRD. Based on the results, it was concluded that Asn803, Tyr809 and Tyr802 along with a water molecule (HOH1001) plays crucial role in binding with inhibitor. It is also proposed that four hits from Life Chemicals database namely, F2276-0099, F2276-0008, F2276-0104 and F2276-0106 could act as potent drug molecules for PCAF BRD. Thus, the present study is strongly believed to have bright impact on rational drug design of potent and novel congeners of PCAF BRD inhibitors.     

Dihydroisocoumarins and Phenylglycosides from Scorzonera longiana,Their Antimicrobial Activities and Molecular Docking Studies

Five new phenyl dihydroisocoumarin glycosides ( 1 – 5 ) and two known compounds ( 6 – 7 ) were identified from the butanol fraction of Scorzonera longiana. The structures of 1 – 7 were elucidated based on spectroscopic methods. Antimicrobial, antitubercular, and antifungal evaluation of compounds 1 – 7 were carried out using the microdilution method against nine microorganisms. Compound 1 was active only against Mycobacterium smegmatis (Ms) with a MIC value of 14.84 μg/mL. All tested compounds ( 1 – 7 ) were active against Ms but only compounds 3–7 were active against fungi (C. albicans, S. cerevisiae) with MIC values of 25.0–125 μg/mL. In addition, molecular docking studies were conducted against Ms DprE1 (PDB ID: 4F4Q), Mycobacterium tuberculosis (Mbt) DprE1 (PDB ID: 6HEZ), and arabinosyltransferase C (EmbC, PDB ID: 7BVE) enzymes. Compounds 2 , 5 , and 7 are the most effective Ms 4F4Q inhibitors. Compound 4 was the most promising inhibitory activity on Mbt DprE with the lowest binding energy of −9,9 kcal/mol.     

Conformational analysis of trimeric maleimide substituted 1,5,9-triazacyclododecane HIV fusion scaffolds

An analysis of the conformational preferences of three trimeric maleimide substituted 1,5,9-triazacyclododecane derivatives, proposed as cross linking reagents for HIV-1 fusion inhibitors, is presented. Exhaustive sampling was performed using the mixed Low Mode Monte Carlo conformational searching technique on the corresponding OPLS2005/GBSA(water) potential energy surface. Geometric structure, molecular length, and hydrogen bonding patterns of the compounds are analyzed. Global minimum energy structures were verified as minima using B3LYP/6-31G1 geometry optimization. All structures adopt a crown-like 12-membered ring conformation; however, the system with the shortest maleimide arms (1a) can also adopt alternative ring orientations. Overall, derivatives with longer maleimide arms were more flexible and resulted in ensembles with a larger number of low energy structures. Comparison with biological inhibition data indicates that there is very little relationship between molecular size and the ability of the scaffold to orient CD4M9 miniproteins for optimal inhibition; however hydrophobicity may play a role.     

Simulation of the different biological activities of diethylstilbestrol (DES) on estrogen receptor alpha and estrogen-related receptor gamma

We describe the application of the molecular dynamics (MD) and molecular mechanics-generalized Born/surface area (MM-GB/SA) approaches to the simulation of the different biological activity of diethylstilbestrol (DES) on two highly homologous nuclear receptors-estrogen receptor alpha (ER-alpha) and estrogen-related receptor gamma (ERR-gamma). DES exerts an agonistic effect against ER-alpha and an antagonistic effect against ERR-gamma. Using the x-ray crystal structures of ER-alpha in the canonical agonist bound form (PDB code: 3ERD) and antagonist bound form (PDB code: 3ERT), ERR-gamma homology models have been constructed for the receptor in two different conformations. MM-GB/SA binding free energy calculations of DES in the ER-alpha and ERR-gamma structures suggest that DES exhibits a greater free energy of binding in the agonist bound conformation of ER-alpha, while the antagonist bound conformation is preferred for ERR-gamma. Further dissection of the free energy contributions coupled with calculation of the ligand binding pocket volume suggests that the van der Waals interactions for DES within the smaller binding pocket volume of ERR-gamma are less favorable and this is the main factor for DES antagonism in ERR-gamma. This approach has potential general applicability to the prediction of the biological activity of nuclear receptor ligands.     

Prediction of protein conformation in water and on surfaces by Monte Carlo simulations using united-atom method

The united-atom method has been used to model an avian pancreatic polypeptide (APP) in water and the adsorption process of an albumin subdomain (AS) onto graphite surface to observe the capability of this lumped modelling approach to generate structures observed in protein data bank (PDB) and from atomistic modelling. The subdomain structure of a protein is simplified by the united-atom approximation where the side chains and peptide groups are represented by lumped spheres. The total potential energy of the adsorption process involves the interaction between these lumped spheres by means of virtual bond chain interaction and the interaction of the spheres with the graphite surface by means of Lennard-Jones potential. The protein/polypeptide structure has been perturbed by Monte Carlo with energy minimisation to obtain the global minimum. Results on the APP in water showed a near-to-experimental PDB conformation revealing the two α-helix structures of this small protein molecule with the root mean square deviation among carbon backbone atoms of 5.9 Å. Protein adsorption on biosurfaces has been made by modelling AS, which has 60 amino acids. The surface is graphite, which is characterised by its hydrophobicity. Graphite was chosen because of its widely used applications in certain implants that interact with blood. Our simulation results showed final conformation close to that obtained by atomistic modelling. It also proved that the whole pattern of intramolecular hydrogen bonds was distorted. The model also demonstrated the random conformation of the original α-helix secondary structures of AS consistent with experimental and atomistic results. While atomistic simulation works well for simulating individual small proteins, the united-atom model is more efficient when simulating macromolecular and multiple protein adsorption where time and limiting computer capacity are key factors.     

MacMolecular: A program for visualization of molecular structures on the Macintosh

MacMolecular displays small- to medium-sized biomolecules, with particular emphasis on peptides. It has been developed to run on color Macintosh computers. The display can be stick, ball and stick, depth cued by thickness stick, or several types of space-filling representations. The program takes input from standard PDB files, simple Cartesian coordinate files, and, in addition, from Kinemage files in which atom information has been included. The program allows color changes of various types as well as the normal functions of translation, rotation, and zooming. In addition, animation files may be produced for subsequent display. Bonding of atoms is done by a distance algorithm (standard) or sequentially to properly display Cα traces and traces of peptides containing simplified representations of amino acids. Stereo viewing is available, and manipulated structures which were drawn from PDB files can be written out to new PDB files. In addition, PICT files of the drawing window can be generated.     

Models of S/pi interactions in protein structures: comparison of the H2S benzene complex with PDB data

S/pi interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H(2)S-benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H(2)S-benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems.     

Descriptor-free molecular discovery in large libraries by adaptive substituent reordering

Molecular discovery often involves identification of the best functional groups (substituents) on a scaffold. When multiple substitution sites are present, the number of possible substituent combinations can be very large. This article introduces a strategy for efficiently optimizing the substituent combinations by iterative rounds of compound sampling, substituent reordering to produce the most regular property landscape, and property estimation over the landscape. Application of this approach to a large pharmaceutical compound library demonstrates its ability to find active compounds with a threefold reduction in synthetic and assaying effort, even without knowing the molecular identity of any compound.     

Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition

Assessment of the evolutionary process is crucial for understanding the effect of protein structure and function on sequence evolution and for many other analyses in molecular evolution. Here, we used simulations to study how taxon sampling affects accuracy of parameter estimation and topological inference in the absence of branch length asymmetry. With maximum-likelihood analysis, we find that adding taxa dramatically improves both support for the evolutionary model and accurate assessment of its parameters when compared with increasing the sequence length. Using a method we call "doppelg?nger trees," we distinguish the contributions of two sources of improved topological inference: greater knowledge about internal nodes and greater knowledge of site-specific rate parameters. Surprisingly, highly significant support for the correct general model does not lead directly to improved topological inference. Instead, substantial improvement occurs only with accurate assessment of the evolutionary process at individual sites. Although these results are based on a simplified model of the evolutionary process, they indicate that in general, assuming processes are not independent and identically distributed among sites, more extensive sampling of taxonomic biodiversity will greatly improve analytical results in many current sequence data sets with moderate sequence lengths.     

Inhibition by phorbol esters of antiimmunoglobulin-induced calcium signalling and B-cell activation

The inhibitory effect of phorbol dibutyrate (PDB) on B-cell stimulation was evaluated using a model in which activation is induced by modest doses of antiimmunoglobulin antibody (anti-Ig) and progression to DNA synthesis is induced by cytochalasin. PDB preferentially inhibited anti-Ig-induced activation and did so during brief (2 hr) preincubation with anti-Ig. Activation was inhibited whether PDB was added before or shortly after anti-Ig. Since activation for cytochalasin responsiveness appears to be mediated by Ca2+, the effect of PDB on the anti-Ig-induced rise in intracellular Ca2+ was evaluated. PDB (and other phorbol esters that activate protein kinase C) inhibited the rise in Ca2+ normally associated with anti-Ig treatment; moreover, PDB reversed an established anti-Ig-induced Ca2+ response. These data suggest that phorbol esters inhibit B-cell activation by interfering with the elevated levels of intracellular Ca2+ produced by cross-linking of surface immunoglobulin by anti-Ig. This could represent a "feedback inhibition" type of response, but it remains to be seen if this occurs under physiological conditions of protein kinase C activation.     

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution

A molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational 'leaps' to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques.     

Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates

In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the "effective number of codons," N(c). Several attempts have been made recently to improve Wright's estimate of N(c), but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of N(c) and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, F, turns out to be a key to the estimation of N(c). F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The N(c) methods that are based on sampling without replacement showed much better accuracy at short gene lengths than those based on sampling with replacement, indicating that Wright's homozygosity method is superior. Surprisingly, the methods based on sampling with replacement displayed a superior correlation with mRNA levels in Escherichia coli.