Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging.

Structural dynamics of human immunodeficiency virus 1 (HIV-1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single-molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV-1. Here, we develope an intact amber-free HIV-1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber-free virions, enabling single-molecule Förster resonance energy transfer (smFRET) studies of click-labeled Env that validated the previous peptide-based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber-free click-labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in-virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.

Influence of Aluminum and Copper on Mechanical Properties of Biocompatible Ti-Mo Alloys: A Simulation-Based Investigation.

The use of titanium and titanium-based alloys in the human body due to their resistance to corrosion, implant ology and dentistry has led to significant progress in promoting new technologies. Regarding their excellent mechanical, physical and biological performance, new titanium alloys with non-toxic elements and long-term performance in the human body are described today. The main compositions of Ti-based alloys and properties comparable to existing classical alloys (C.P. TI, Ti-6Al-4V, Co-Cr-Mo, etc.) are used for medical applications. The addition of non-toxic elements such as Mo, Cu, Si, Zr and Mn also provides benefits, such as reducing the modulus of elasticity, increasing corrosion resistance and improving biocompatibility. In the present study, when choosing Ti-9Mo alloy, aluminum and copper (Cu) elements were added to it. These two alloys were chosen because one element is considered a favorable element for the body (copper) and the other element is harmful to the body (aluminum). By adding the copper alloy element to the Ti-9Mo alloy, the elastic modulus decreases to a minimum value of 97 GPa, and the aluminum alloy element increases the elastic modulus up to 118 GPa. Due to their similar properties, Ti-Mo-Cu alloys are found to be a good optional alloy to use.

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

The string method with swarms of trajectories (SMwST) is an algorithm that identifies a physically meaningful transition pathway─a one-dimensional curve, embedded within a high-dimensional space of selected collective variables. The SMwST algorithm leans on a series of short, unbiased molecular dynamics simulations spawned at different locations of the discretized path, from whence an average dynamic drift is determined to evolve the string toward an optimal pathway. However conceptually simple in both its theoretical formulation and practical implementation, the SMwST algorithm is computationally intensive and requires a careful choice of parameters for optimal cost-effectiveness in applications to challenging problems in chemistry and biology. In this contribution, the SMwST algorithm is presented in a self-contained manner, discussing with a critical eye its theoretical underpinnings, applicability, inherent limitations, and use in the context of path-following free-energy calculations and their possible extension to kinetics modeling. Through multiple simulations of a prototypical polypeptide, combining the search of the transition pathway and the computation of the potential of mean force along it, several practical aspects of the methodology are examined with the objective of optimizing the computational effort, yet without sacrificing accuracy. In light of the results reported here, we propose some general guidelines aimed at improving the efficiency and reliability of the computed pathways and free-energy profiles underlying the conformational transitions at hand.

Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding.

Human fibroblast growth factor (FGF) 1 or hFGF1 is a member of the FGF family that is involved in various vital processes such as cell proliferation, cell differentiation, angiogenesis, and wound healing. hFGF1, which is associated with low stability in vivo, is known to be stabilized by binding heparin sulfate, a glycosaminoglycan that aids the protein in the activation of its cell surface receptor. The poor thermal and proteolytic stability of hFGF1 and the stabilizing role of heparin have long been observed experimentally; however, the mechanistic details of these phenomena are not well understood. Here, we have used microsecond-level equilibrium molecular dynamics (MD) simulations to quantitatively characterize the structural dynamics of monomeric hFGF1 in the presence and absence of heparin hexasaccharide. We have observed a conformational change in the heparin-binding pocket of hFGF1 that occurs only in the absence of heparin. Several intramolecular interactions were also identified within the heparin-binding pocket that form only when hFGF1 interacts with heparin. The loss of both intermolecular and intramolecular interactions in the absence of heparin plausibly leads to the observed conformational change. This conformational transition results in increased flexibility of the heparin-binding pocket and provides an explanation for the susceptibility of apo hFGF1 to proteolytic degradation and thermal instability. This study provides a glimpse into mechanistic details of the heparin-mediated stabilization of hFGF1 and encourages the use of microsecond-level MD in studying the effect of binding on protein structure and dynamics. In addition, the observed differential behavior of hFGF1 in the absence and presence of heparin provides an example, where microsecond-level all-atom MD simulations are necessary to see functionally relevant biomolecular phenomena that otherwise will not be observed on sub-microsecond time scales.

Activities and polymorphisms of MMP-2 and MMP-9, smoking, diabetes and risk of prostate cancer.

Matrix metalloproteinases (MMPs) are a group of zinc dependent enzymes that are involved in tumor cell invasion and metastasis. The role of MMP-2 and -9 genetic polymorphism in different malignancies has been the subject of numerous studies. The present research has attempted to discover any positive correlation between MMP-2 and MMP-9 SNPs and prostate cancer (PCa) in patients with a history of either diabetes or smoking habits. 112 PCa-patients and 150 unrelated healthy-controls that matched for age and sex were selected for present case-control study. MMP-2 -1575G/A and MMP-9 -1562 C/T polymorphisms detected by PCR-RFLP, serum tissue inhibitors of metalloproteinases (TIMP-1 and TIMP-2), testosterone, prostate-specific antigen (PSA), free-prostate-specific-antigen (fPSA), and fPSA/PSA levels were detected by ELISA and enzyme assay, respectively. MMP-2 and MMP-9 activities were measured by gelatin-zymography. Covariates were considered as age, status of cigarette smoking, and a possible history of diabetes mellitus (DM). The frequency of -1575 MMP-2 A/A + A/G and -1562 MMP-9 C/T + T/T genotypes were higher in PCa-patients with DM (74.3%,p = 0.003) and with smoking habits (72.5%,p = 0.005). These genotypes were associated with the increased risk of prostate cancer in smokers (3.52-folds) and in individuals with history of DM (4.34-folds). A significant positive association was found between level of TIMPs (TIMP -1 and TIMP-2) and BMI in PCa-patients and also between testosterone levels and MMP-9 activity in healthy control subjects. For the first time, this study demonstrated that activities of MMP-2 -1575G/A and MMP-9 -1562C/T variants in association with smoking and diabetes are considered significant risk factors for PCa.

Experimental and Numerical Study of AISI 4130 Steel Surface Hardening by Pulsed Nd:YAG Laser.

Laser surface transformation hardening (LSTH) of AISI 4130 was investigated by a Nd:YAG pulsed laser. Laser focal height (LFH), pulse width (LPW), scanning speed (LSS), and power (LP) varied during the experiments. The microstructure of the treated zone was characterized by optical (OM) and field emission scanning electron microscopy (FESEM). Micro-hardness was measured in the width and depth directions. Results showed that the hardness and depth of hardened layer increased by decreasing the LSS and the laser focal position (LFP), and by increasing the LPW. The results were compared with those obtained by furnace heat treatment of the same steel. Eventually, a finite element model was employed for the simulation of the LSTH of AISI 4130 steel and calculation of the heat-treated zone. The results showed that the model can predict with accuracy the temperature profile and the size and the shape of the laser hardened region.

ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation.

Profilin-1 (PFN1) is a 140-amino-acid protein with two distinct binding sites-one for actin and one for poly-L-proline (PLP). The best-described function of PFN1 is to catalyze actin elongation and polymerization. Thus far, eight DNA mutations in the PFN1 gene encoding the PFN1 protein are associated with human amyotrophic lateral sclerosis (ALS). We and others recently showed that two of these mutations (Gly118Val or G118V and Cys71Gly or C71G) cause ALS in rodents. In vitro studies suggested that Met114Thr and Thr109Met cause the protein to behave abnormally and cause neurotoxicity. The mechanism by which a single amino acid change in human PFN1 causes the degeneration of motor neurons is not known. In this study, we investigated the structural perturbations of PFN1 caused by each ALS-associated mutation. We used molecular dynamics simulations to assess how these mutations alter the secondary and tertiary structures of human PFN1. Herein, we present our in silico data and analysis on the effect of G118V and T109M mutations on PFN1 and its interactions with actin and PLP. The substitution of valine for glycine reduces the conformational flexibility of the loop region between the α-helix and ß-strand and enhances the hydrophobicity of the region. Our in silico analysis of T109M indicates that this mutation alters the shape of the PLP-binding site and reduces the flexibility of this site. Simulation studies of PFN1 in its wild type (WT) and mutant forms (both G118V and T109M mutants) revealed differential fluctuation patterns and the formation of salt bridges and hydrogen bonds between critical residues that may shed light on differences between WT and mutant PFN1. In particular, we hypothesize that the flexibility of the actin- and PLP-binding sites in WT PFN1 may allow the protein to adopt slightly different conformations in its free and bound forms. These findings provide new insights into how each of these mutations in PFN1 might increase its propensity for misfolding and aggregation, leading to its dysfunction.

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

ATP synthase is the most prominent bioenergetic macromolecular motor in all life forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling and high-performance free-energy methods, the sequence of conformational transitions involved in a functional cycle accompanying ATP hydrolysis has been investigated in unprecedented detail over an aggregate simulation time of 65 µs. Our simulated pathways reveal that the chemical energy produced by ATP hydrolysis is harnessed via the concerted motion of the protein-protein interfaces in the V1-ring, and is nearly entirely consumed in the rotation of the central stalk. Surprisingly, in an ATPase devoid of a central stalk, the interfaces of this ring are perfectly designed for inducing ATP hydrolysis. However, in a complete V1-ATPase, the mechanical property of the central stalk is a key determinant of the rate of ATP turnover. The simulations further unveil a sequence of events, whereby unbinding of the hydrolysis product (ADP + Pi) is followed by ATP uptake, which, in turn, leads to the torque generation step and rotation of the center stalk. Molecular trajectories also bring to light multiple intermediates, two of which have been isolated in independent crystallography experiments.

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations.

We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.

Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases?

We have characterized the conformational ensembles of polyglutamine Qn peptides of various lengths n (ranging from 6 to 40), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For Q40 (i.e., just above the pathological length ≃36 for Huntington's disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible α-helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including ß- and α-strands, and ß- and α-hairpins. Most importantly, for Q40 we find that there exists a long-range correlation (ranging for at least 20 residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most 5 residues apart). Adding a C-terminal hexaproline to Q40 suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena.

PPII propensity of multiple-guest amino acids in a proline-rich environment.

There has been considerable debate about the intrinsic PPII propensity of amino acid residues in denatured polypeptides. Experimentally, this scale is based on the behavior of guest amino acid residues placed in the middle of proline-based hosts. We have used classical molecular dynamics simulations combined with replica-exchange methods to carry out a comprehensive analysis of the conformational equilibria of proline-based host oligopeptides with multiple guest amino acids including alanine, glutamine, valine, and asparagine. The tracked structural characteristics include the secondary structural motifs based on the Ramachandran angles and the cis/trans isomerization of the prolyl bonds. In agreement with our recent study of single amino acid guests, we did not observe an intrinsic PPII propensity in any of the guest amino acids in a multiple-guest setting. Instead, the experimental results can be explained in terms of (i) the steric restrictions imposed on the C-terminal guest amino acid that is immediately followed by a proline residue and (ii) an increase in the trans content of the prolyl bonds due to the presence of guest residues. In terms of the latter, we found that the more guests added to the system, the larger the increase in the trans content of the prolyl bonds, which results in an effective increase in the PPII content of the peptide.

A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides.

There has been considerable debate about the intrinsic PPII propensity of amino-acid residues in denatured polypeptides. Experimentally, the propensity scale is based on the behavior of guest amino-acid residues placed in the middle of polyproline hosts. We have used classical molecular dynamics simulations, with state-of-the-art force fields to carry out a comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests. The tracked structural characteristics include the PPII content, the cis/trans isomerization of the prolyl bonds, the puckering of the pyrrolidine rings of the proline residues, and the secondary structural motifs. We find no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. Instead, the PPII content as derived from experiments may be explained in terms of: 1), a local correlation between the dihedral angles of the guest amino acid and the proline residue immediately preceding it; and 2), a nonlocal correlation between the cis/trans states of the peptide bonds. In terms of the latter, we find that the presence of a guest (other than proline, tyrosine, or tryptophan) increases the trans content of most of the prolyl bonds, which results in an effective increase of the peptide PPII content. With respect to the local dihedral correlations, we find that these are well described in terms of the so-called odds-ratio statistic. Expressed in terms of free energy language, the PPII content based on the odds-ratio of the relevant residues correlate well with the experimentally measured PPII content.

A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers.

Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)(n)-Nme, n=2,3, ... ,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method--which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables--combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n=2, ... ,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.

Conformations and free energy landscapes of polyproline peptides.

The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle omega, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.

Effect of cigarette smoke on spermatogenesis in rats.

INTRODUCTION: The aim of this study was to evaluate the process of spermatogenesis in rats exposed to the cigarette smoke. MATERIALS AND METHODS: Thirty adult male rats were divided into 2 groups of cases and controls. An apparatus made especially for this study was used to produce smoke from a commonly used cigarette and expose the rats to the smoke. The rats in the case group were exposed to the cigarette smoke for 10 weeks (90 minutes every day for 6 days in each week). The rats in the control group were meanwhile in the fresh room air. RESULTS: Development of the sperms was mildly reduced in 14 (93.3%) and 4 (26.7%) rats in the case and control groups, respectively (P < .001). The mean average diameter of the seminiferous tubules was reported to be 0.421 +/- 0.097 mm and 0.493 +/- 0.026 mm in the case and control groups, respectively (P = .04). The mean numbers of Sertoli cells were 9.2 +/- 1.2 and 13.3 +/- 1.8 in the case and control groups, respectively (P < .001). A concurrent reduction in the number of germ cells and Leydig cells with the decrease in the number of Sertoli cells was seen in the rats of the case group. CONCLUSION: Cigarette smoke has a rather obvious effect on spermatogenesis in rats which may be due to toxic substances in the cigarette or the histologic reactions due to hypoxemia induced by smoke. Although further documentation, especially in humans is required, the potential impact of smoking on fertility in men should be considered in public health education.

Pediatric cystine calculi in west of Iran: a study of 22 cases.

INTRODUCTION: Cystinuria is an autosomal recessive disorder which clinically presents as cystine calculi. In this study, we reviewed cystine calculi cases in the west of Iran to determine their common presentations and response to different therapeutic modalities. MATERIALS AND METHODS: Between 1999 and 2005, we had 22 pediatric patients (11 boys and 11 girls) with cystine calculi. The demographic characteristics and clinical data of the patients as well as the treatment results were reviewed. RESULTS: The mean age of the patients was 34.20 +/- 42.99 months (range, 4 to 156 months). They were followed for a mean duration of 23 months (range, 3 to 70 months). Thirteen patients (59.1%) had bilateral and 9 (41%) had unilateral kidney calculi. The sizes of the calculi were between 2 mm and 20 mm. Nine patients (41%) had renal atrophic changes and 1 (4.5%) had obstructive acute renal failure. Hydration and urinary alkalinization were administrated to all of the patients which yielded an excellent result in 54.5% and a poor response in 27.2%. Captopril started for 5 patients was effective only in 1. D-penicillamine had no favorable response. Extracorporeal shockwave lithotripsy was successful in 5 attempts and failed in 4. Surgical interventions were performed for 13 patients (59.1%) and 6 (27.2%) required more than 1 surgical operation. CONCLUSION: We recommend metabolic workup of childhood urolithiasis and appropriate medical management of its underlying disease. We also recommend minimally invasive urologic techniques including shockwave lithotripsy only when there are clear indications for nonmedical procedures.