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The recently developed statistical measure for the type of residue-residue contact at protein complex interfaces, based on a parameter-free definition of contact, has been used to define a contact score that is correlated with the likelihood of correctness of a proposed complex structure. Comparing the proposed contact scores on the native structure and on a set of model structures the proposed measure was shown to generally favor the native structure but in itself was not able to reliably score the native structure to be the best. Adjusting the scores of redocking experiments with the contact score showed that the adjusted score was able to move up the ranking of the native-like structure among the proposed complexes when the native-like was not ranked the best by the respective program. Tests on docking of unbound proteins compared the contact scores of the complexes with the contact score of the crystal structure again showing the tendency of the contact score to favor native-like conformations. The possibility of using the contact score to improve the determination of biological dimers in a crystal structure was also explored. Proteins 2017; 85:235-241. © 2016 Wiley Periodicals, Inc.

The objective of this study was to develop an in silico screening model for characterization of potential novel ligands from commercial drug libraries able to functionally activate certain olfactory receptors (ORs), which are members of the class A rhodopsin-like family of G protein couple receptors (GPCRs), in the brain of murine models of concussion. We previously found that concussions may significantly influence expression of certain ORs, for example, OR4M1 in subjects with a history of concussion/traumatic brain injury (TBI). In this study, we built a 3-D OR4M1 model and used it in in silico screening of potential novel ligands from commercial drug libraries. We report that in vitro activation of OR4M1 with the commercially available ZINC library compound 10915775 led to a significant attenuation of abnormal tau phosphorylation in embryonic cortico-hippocampal neuronal cultures derived from NSE-OR4M1 transgenic mice, possibly through modulation of the JNK signaling pathway. The attenuation of abnormal tau phosphorylation was rather selective since ZINC10915775 significantly decreased tau phosphorylation on tau Ser202/T205 (AT8 epitope) and tau Thr212/Ser214 (AT100 epitope), but not on tau Ser396/404 (PHF-1 epitope). Moreover, no response of ZINC10915775 was found in control hippocampal neuronal cultures derived from wild type littermates. Our in silico model provides novel means to pharmacologically modulate select ubiquitously expressed ORs in the brain through high affinity ligand activation to prevent and eventually to treat concussion induced down regulation of ORs and subsequent cascade of tau pathology. J. Cell. Biochem. 117: 2241-2248, 2016. © 2016 Wiley Periodicals, Inc.

Dynamic characteristics of protein surfaces are among the factors determining their functional properties, including their potential participation in protein-protein interactions. The presence of clusters of static residues-"stability patches" (SPs)-is a characteristic of protein surfaces involved in intermolecular recognition. The mechanism, by with SPs facilitate molecular recognition, however, remains unclear. Analyzing the surface dynamic properties of the growth hormone and of its high-affinity variant we demonstrated that reshaping of the SPs landscape may be among the factors accountable for the improved affinity of this variant to the receptor. We hypothesized that SPs facilitate molecular recognition by moderating the conformational entropy of the unbound state, diminishing enthalpy-entropy compensation upon binding, and by augmenting the favorable entropy of desolvation. SPs mapping emerges as a valuable tool for investigating the structural basis of the stability of protein complexes and for rationalizing experimental approaches, such as affinity maturation, aimed at improving it.

Targeted therapeutic intervention in receptor-ligand interactions of p53 mediated tumor suppression can impact progression of disease, aging, and variation in genetic expression. Here, we conducted a number of molecular simulations, based on structures of p53 in complex with its transcriptional co-activating CBP bromodomain, determined by NMR spectroscopy, to investigate the energetics of the binding complex. Building on the observation that acetylation of K382 in p53 serves as the essential triggering switch for a specific interaction with CBP, we assessed the differential effect of acetylation on binding from simulations of an octapeptide derived from p53 with acetylated and non-acetylated K382 (residues 379-386). Cluster analysis of the simulations shows that acetylation of the free peptide does not significantly change the population of the preferred conformation of the peptide in solution for binding to CBP. Conversion of the acetylated K382 to non-acetylated form with Free Energy Perturbation (FEP) simulations of the p53•CBP complex and the free peptide showed that the relative contribution of the acetyl group to binding is 4.8 kcal/mol. An analysis of residue contributions to the binding energy using an MM-GBSA approach agrees with the FEP results and sheds additional light on the origin of selectivity in p53 binding to the CBP bromodomain.

In aqueous solution, the ensemble of conformations sampled by peptides and unfolded proteins is largely determined by their interaction with water. It has been a long-standing goal to capture these solute-water energetics accurately and efficiently in calculations. Historically, accessible surface area (ASA) has been used to estimate these energies, but this method breaks down when applied to amphipathic peptides and proteins. Here we introduce a novel method in which hydrophobic ASA is determined after first positioning water oxygens in hydrogen-bonded orientations proximate to all accessible peptide/protein backbone N and O atoms. This conditional hydrophobic accessible surface area is termed CHASA. The CHASA method was validated by predicting the polyproline-II (P(II)) and beta-strand conformational preferences of non-proline residues in the coil library (i.e., non-alpha-helix, non-beta-strand, non-beta-turn library derived from X-ray elucidated structures). Further, the method successfully rationalizes the previously unexplained solvation energies in polyalanyl peptides and compares favorably with published experimentally determined P(II) residue propensities. We dedicate this paper to Frederic M. Richards.

Uroporphyrinogen III synthase (URO-synthase) catalyzes the cyclization and D-ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO-synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein-protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane-synthase (HMB-synthase) and/or uroporphyrinogen-decarboxylase (URO-decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically-labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO-synthase backbone (13)C(alpha) (100%), (1)H(alpha) (99.6%), and nonproline (1)H(N) and (15)N resonances (94%) was achieved as well as 85% of the side-chain (13)C and (1)H resonances. NMR analyses of URO-synthase titrated with competitive inhibitors N(D)-methyl-1-formylbilane (NMF-bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO-synthase crystal structure with NMF-bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme-inhibitor complex. The absence of chemical shift changes in the (15)N spectrum of URO-synthase mixed with the homogeneous HMB-synthase holoenzyme or URO-decarboxylase precluded occurrence of a stable cytosolic enzyme complex.

Recent studies have indicated that the unfolded states of polypeptides contain a sub- stantial amount of polyproline type II (PII) struc- ture. This energetically and structurally preorga- nized state may contribute to the reduction of the folding search, as well as to the recognition of intrinsically unstructured proteins and polyproline ligands. Using Monte Carlo simulations of natively unfolded peptides in the presence of explicit aque- ous solvation, we observe that residue-specific PII conformational propensity is the result of the modu- lation of polypeptide backbone hydration by a proxi- mal side-chain. Such a mechanism may be unique among those that contribute to the modulation of secondary structures in proteins. The calculated conformational propensities should prove useful for the development of a configurational PII scale neces- sary for the prediction and design of natural-like polypeptides. Proteins 2005;61:769 -776.

An effort was made to discover mast cell degranulating (MCD) peptide analogs that bind with high affinity to mast cell receptors without triggering secretion of histamine or other mediators of the allergic reaction initiated by immunoglobulin E (IgE) after mast cell activation. Such compounds could serve as inhibitors of IgE binding to mast cell receptors. An alanine scan of MCD peptide reported previously showed that the analog [Ala12]MCD was 120-fold less potent in histamine-releasing activity and fivefold more potent in binding affinity to mast cell receptors than the parent MCD peptide. Because this analog showed marginal intrinsic activity and good binding affinity it was subsequently tested in the present study as an IgE inhibitor. In contrast to MCD peptide, [Ala12]MCD showed a 50% inhibition of IgE binding to the Fc epsilon RI alpha mast cell receptor by using rat basophilic leukemia (RBL-2H3) mast cells and fluorescence polarization. Furthermore, in a beta-hexosaminidase secretory assay, the peptide also showed a 50% inhibition of the secretion of this enzyme caused by IgE. An attempt was made to relate structural changes and biologic differences between the [Ala12]MCD analog and the parent MCD peptide. The present results show that [Ala12]MCD may provide a base for designing agents to prevent IgE/Fc epsilon RI alpha interactions and, consequently, allergic conditions.

It is shown that, by optimizing the placement of a solute in a solvent droplet or in a periodic simulation cell, the number of solvent molecules can be reduced without affecting the quality of the simulation. Q 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 812]815, 1997

An iso-energy cutoff scheme is introduced for the calculation of the potential of mean force between two ions in water. The cutoff criterion is based on the optimal interaction of the water dipole with the ion pair, for which analytical expressions are derived. Formulas are also derived to characterize the solvent reorganization contribution to the potential of mean force. Treatment of the contributions from waters outside the cutoff is also discussed. © 1994 John Wiley & Sons, Inc.

as well as its range of appli- cability in conjunction with Monte Carlo computer simulations using thermodynamic integration based on Gaussian quadratures. The technique employed is compared with the slow growth method (an other vari- ant of thermodynamic integration), with the perturbation method and with the use of the grand-canonical ensemble. INTRODUCTION AND BACKGROUND The calculation of the free energy, long recognized as a computationally exacting task, is of special importance due to the role of the free energy in determininig chemical equilibria. As reviewed recently, 1 4 free energy simulation techniques are characterized by the path selected that connects the two systems in the configuration space (e.g. the choice of the coupling parameter, vide infra) and by the quantity chosen whose Boltzmann average is related to the free energy — with the exception of calculations in the grand-canonical ensemble where the chemical potential is fixed at the outset. The various choices of the coupling parameter, described in detail in ref. 2, fall into two distinct classes

Alkylation of the sugar-phosphate backbone of DNA can result upon exposure to several potent carcinogens, inducing DNA misfunction. In order to assess the structural and energetic changes in DNA helices induced by such alkylation, we have performed AMBER-based analyses on phosphotriester containing analogues of (d-[GGAATTCC])2. Fourteen analogues of the nonalkylated oligomer were examined, each bearing a single alkylation of known stereochemistry. Results indicate that although there is minimal effect on the aromatic bases, the presence of a phosphotriester disturbs the sugar-phosphate backbone in complex ways. For most analogues, total minimum energies are lower for the Sp-alkylations than for the Rp-alkylations which point directly into the major groove of the helix; however, different energetic contributions follow different, or no, trends in dependence on alkylation site and/or stereochemistry. Where data is available, experimental nmr results agree with the calculations reported here.

Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C7, C5, αR, and PII conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C7 to C5, αR, and PII are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C7 conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C7, αR, and PII are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl-water hydrogen bond in C5, αR, and PII competes successfully with the intramolecular NH…OC interaction in C7.

A numerical procedure is described and tested for the determination of solvent sites in a crystal hydrate from computer simulation results. The method does not require the computation of density distributions.

The internal energies of hydration of the Ala dipeptide in the C7, C5, αR, and PII conformations were computed with the Monte Carlo method. The results indicate that both the αR and PII conformations are preferentially stabilized by hydration in general accord with the results of recent experiments described by Madison and Kopple. The major contributing factor for the stability of internal energy of hydration for these conformations can be traced to the hydration of the carbonyl group.

A series of liquid state Monte Carlo computer simulations on the N-methyl acetamide in water (NMA molecule) are described, considering both the cis and trans isomeric forms of NMA. Two independent sets of calculations were performed, one set based on the potential functions developed by Clementi and co-workers (CPF) used in conjunction with the Matsuoka et al. (MCY) water-water potential, and the other set using the OPLS potential of Jorgensen and coworkers for solute-water interactions and the TIP4P potential for the water-water interactions. The relative hydration energies of the cis and trans isomers of NMA and the transfer energies of NMA from free space to water are discussed with respect to the convergence level of the simulations and the sensitivity of results to the choice of the intermolecular potential functions. The structural chemistry of the aqueous hydration for NMA is developed from the simulation result based on Proximity Analysis. The sensitivity of the structural and energetic indices of analysis to choice of potential is described. Preliminary results of the calculation of the hydration contribution to the free energy are also presented.

Monte Carlo computer simulations were performed on dilute aqueous solutions of the dimethylphosphate anion and the sodium dimethylphosphate ion pair, with the two phosphodiester torsional angles in the gauche–gauche, gauche–trans, and trans–trans conformations. The structural and energetic aspects of the aqueous hydration of each molecule were analyzed in terms of quasi component distribution functions based on the proximity criterion and partitioned into ionic, hydrophilic, and hydrophobic contributions to facilitate an understanding of the hydration pattern and conformational trends in these multifunctional solutes. Special attention was also paid to methodological issues affecting hydration, such as statistical uncertainty in the determined hydration indices, choice of partial atomic charges for the solute atoms, and solute–water interaction potentials adopted in the simulations. The results showed that gauche–trans and gauche–gauche forms are equally favorable for the dimethylphosphate anion with the trans extended form destabilized by hydration. The sodium dimethylphosphate ion pair hydration energetically favors the trans–trans conformation.

The relative free energias of hydration of dimethyl phosphate anion in gauchegauche, gauchetrans, and trans-trans conformations of phosphodiester torsion angles, computed with Monte Carlo method in the (T, V, N) ensemble at 25 OC, are reported. The free energy differences are determined by the probability ratio method using both umbrella sampling with harmonic weighting functions and adaptive umbrella sampling technique. The results indicate a stability trend of gg > gt > tt for the phosphodiester torsions in aqueous solutions. The magnitude of the conformational differences indicates the extended gt and tt conformations to be thermally accessible to some extent at ambient temperatures. Conclusions of the present study are in agreement with the IR and Raman inferences and "P NMR investigations. Methodologically, the performance of the free energy simulations through probability ratio method along with the adaptive umbrella sampling technique is tested on a three-legged thermocycle and found to converge in a satisfactory manner.

Calculs de Monte Carlo sur l'ensemble (T,V,N) pour des solutions aqueuses diluees de benzene, avec des potentiels de paire determines par les methodes quantiques: la 1ere couche d'hydratation comprend 23 molecules H 2 O; l'hydratation dans le plan est hydrophobe