Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima

Dihedral principal component analysis (dPCA) has recently been developed and shown to display complex features of the free energy landscape of a biomolecule that may be absent in the free energy landscape plotted in principal component space due to mixing of internal and overall rotational motion that can occur in principal component analysis (PCA) [Mu et al., Proteins: Struct Funct Bioinfo 2005;58:45-52]. Another difficulty in the implementation of PCA is sampling convergence, which we address here for both dPCA and PCA using a tetrapeptide as an example. We find that for both methods the sampling convergence can be reached over a similar time. Minima in the free energy landscape in the space of the two largest dihedral principal components often correspond to unique structures, though we also find some distinct minima to correspond to the same structure.     

Tick‐borne viruses: Current trends in large‐scale viral surveillance

Ticks are ectoparasites that transmit pathogens, such as tick‐borne viruses, to their hosts. Tick‐borne viruses are diverse: they can be categorized into two orders, nine families, and at least 12 genera. Almost 25% of these viruses are infectious to humans and some are a serious threat to public health. The global rise in tick‐borne virus diseases has been linked to climate change which has reduced tick mortality in the winter and extended their active period. The spread of tick‐borne viral diseases to humans has received significant interest due to the increased threat to human life; epidemiological monitoring of tick‐borne viruses using molecular, immunological, and environmental methods is now a priority. Nevertheless, many tick‐borne diseases remain undiagnosed, which poses a challenge to public administration and health care officials. This review discusses three major tick‐borne RNA viruses that cause serious infection in humans: severe fever with thrombocytopenia syndrome (SFTS) virus, tick‐borne encephalitis (TBE), and Crimean–Congo hemorrhagic fever (CCHF) virus. Specifically, we discuss the epidemiological monitoring, vector control measures, molecular diagnostics, vaccines, and environmental determinants related to these viruses. Furthermore, we review the current surveillance of these tick‐borne viruses with a specific focus on diagnostic approaches that employ molecular interventions such as viral nucleic acid isolation, PCR‐based diagnostics, and high‐throughput sequencing technologies.     

Structural and dynamical properties of KTS‐disintegrins: A comparison between Obtustatin and Lebestatin

Obtustatin and Lebestatin are lysine‐threonine‐serine (KTS)‐disintegrins, which are a family of low molecular weight polypeptides present in many viperidae venoms and are potent and specific inhibitors of collagen‐binding integrins. The integrin binding loop, harboring the ²¹KTS²³ motif, and the C‐terminal tail are known to be responsible for the selective binding to the α1β1 integrin. Despite a very high sequence homology (only two mutations are present in Lebestatin relative to Obtustatin, namely R24L and S38L), Lebestatin exhibits a higher inhibitory effect than Obtustatin on cell adhesion and cell migration to collagens I and IV. Here we show, by means of molecular dynamics simulations of the two polypeptides in aqueous solution, that Lebestatin possesses a higher flexibility of the C‐terminal tail and a greater solvent accessibility of the integrin binding loop than Obtustatin. It may be hypothesized that these properties may contribute to the higher binding‐affinity of Lebestatin to its biological partner. © 2012 Wiley Periodicals, Inc.     

Assembling viral channel forming proteins: Vpu from HIV‐1

Different routes of assembly are probed for the transmembrane domain (TMD) of the bitopic membrane protein Vpu from HIV‐1. Vpu is responsible for the amplification of viral release from the host cell. The mode of action includes (i) heteroassembly with host factors and (ii) the formation of homo‐oligomers, which are able to conduct ions across the lipid membrane. Two different routes of assembling short sequences of the N terminus, including the TMD of Vpu, Vpu_1–32, and Vpu_8–26, are presented by using a combination of classical molecular dynamics (MD) simulations combined with a docking approach. The rim of alanines (Ala‐8, ‐11, ‐15, and ‐19) resembles an interlocking motif for the sequential assembly into a dimer and trimer. Simultaneous assembly results in oligomeric bundles (trimers to pentamers) with either tryptophans (Trp‐23) or purely hydrophobic residues facing the center. Bundles, with serines facing the pore (Ser‐24), are energetically not the lowest structures. For pentameric bundles with Ser‐24 facing the pore, no water column develops during a short 25 ns MD simulation. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 517–529, 2013.     

Effect of head‐to‐tail cyclization on conformation of histatin‐5

Histatin‐5 (Hst‐5, DSHAKRHHGYKRKFHEKHHSHRGY) is a member of a histidine‐rich peptide family secreted by major salivary glands, exhibiting high fungicidal activity against Candida albicans. In the present work, we demonstrate the 3D structure of the head‐to‐tail cyclic variant of Hst‐5 in TFE solution determined using NMR spectroscopy and molecular dynamics simulations. The cyclic histatin‐5 reveals a helix‐loop‐helix motif with α‐helices at positions Ala⁴‐His⁷ and Lys¹¹‐Ser²⁰. Both helical segments are arranged relative to each other at an angle of ca. 142°. The head‐to‐tail cyclization increases amphipathicity of the peptide, this, however, does not affect its antimicrobial potency. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

A step toward the prediction of the fluorescence lifetimes of tryptophan residues in proteins based on structural and spectral data

A method is presented that allows the calculation of the lifetimes of tryptophan residues on the basis of spectral and structural data. It is applied to two different proteins. The calcium binding protein from the sarcoplasm of the muscles of the sand worm Nereis diversicolor (NSCP) changes its conformation upon binding of Ca2+ or Mg2+. NSCP contains three tryptophan residues at position 4, 57, and 170, respectively. The fluorescence lifetimes of W57 are investigated in a mutant in which W4 and W170 have been replaced. The time resolved fluorescence properties of W57 are linked to its different microconformations, which were determined by a molecular dynamics simulation map. Together with the determination of the radiative rate constant from the wavelength of maximum intensity of the decay associated spectra, it was possible to determine an exponential relation between the nonradiative rate constant and the distance between the indole CE3 atom and the carbonyl carbon of the peptide bond reflecting a mechanism of electron transfer as the main determinant of the value for the nonradiative rate constant. This result allows the calculation of the fluorescence lifetimes from the protein structure and the spectra. This method was further tested for the tryptophan of Ha-ras p21 (W32) and for W43 of the Tet repressor, which resulted in acceptable values for the predicted lifetimes.     

Climate change and large‐scale human population collapses in the pre‐industrial era

Aim It has long been assumed that deteriorating climate (cooling and warming above the norm) could shrink the carrying capacity of agrarian lands, depriving the human population of sufficient food. Population collapses (i.e. negative population growth) follow. However, this human–ecological relationship has rarely been verified scientifically, and evidence of warming‐caused disaster has never been found. This research sought to explore quantitatively the temporal pattern, spatial pattern and triggers of population collapses in relation to climate change at the global scale over 1100 years. Location Various countries/regions in the Northern Hemisphere (NH) during the pre‐industrial era. Methods We performed time‐series analysis to examine the association between temperature change and country‐wide/region‐wide population collapses in different climatic zones. All of the known population collapse incidents in the NH in the period ce 800–1900 were included in our data analysis. Results Nearly 90% of population collapses in various NH countries/regions occurred during periods of climate deterioration characterized by shrinking carrying capacity of the land. In addition, we found that cooling dampened the human ecosystem and brought about 80% of the collapses in warmer humid, cooler humid and dry zones, while warming adversely affected the ecosystems in dry and tropical humid zones. All of the population collapses and growth declines in periods of warm climate occurred in dry and tropical humid zones. Malthusian checks (famines, wars and epidemics) were the dominant triggers of population collapses, which peaked dramatically when climate deteriorated. Main conclusions Global demographic catastrophes and most population collapse incidents occurred in periods with great climate change, owing to overpopulation caused by diminished carrying capacity of the land and the resultant outbreak of Malthusian checks. Impacts of cooling or warming on land carrying capacity varied geographically, as a result of the diversified ecosystems in different parts of the Earth. The observed climate–population synchrony challenges Malthusian theory and demonstrates that it is not population growth alone but climate‐induced subsistence shortage and population growth working synergistically, that cause large‐scale human population collapses on the long‐term scale.     

Smoluchowski dynamics of the vnd/NK‐2 homeodomain from Drosophila melanogaster: First‐order mode‐coupling approximation

This work is the first in a series devoted to applying mode coupling diffusion theory to the derivation of local dynamics properties of proteins in solution. The first‐order mode‐coupling approximation, or optimized Rouse–Zimm local dynamics (ORZLD), is applied here to derive the rotational dynamics of the bonds and compare the calculated with the experimental nmr ¹⁵N spin–lattice relaxation time behavior of the vnd/NK‐2 homeodomain from Drosophila melanogaster. The starting point for the calculations is the experimental three‐dimensional structure of the homeodomain determined by multidimensional nmr spectroscopy. The results of the computations are compared with experimentally measured ¹⁵N spin–lattice relaxation times T₁, at 34.5 and 60.8 MHz, to check the first‐order approximation. To estimate the relative importance of internal and overall rotation, both rigid and fluctuating dynamic models are examined, with fluctuations evaluated using molecular dynamics (MD) simulations. The correlation times for the fundamental bond vector time correlation function and for the second‐order bond orientational TCF are obtained as a function of the residue number for vnd/NK‐2. The stability of the corresponding local dynamics pattern for the fluctuating structure as a function of the length of the MD trajectory is presented. Diffusive dynamics, which is essentially free of model parameters even at first order in the mode‐coupling diffusion approach, confirm that local dynamics of proteins can be described in terms of rotational diffusion of a fluctuating quasi‐rigid structure. The comparison with the nmr data shows that the first‐order mode coupling diffusion approximation accounts for the correct order of magnitude of the results and of important qualitative aspects of the data sensitive to conformational changes. Indications are obtained from this study to efficiently extend the theory to higher order in the mode‐coupling expansion. These results demonstrate the promise of the mode‐coupling approach, where the local dynamics of proteins is described in terms of rotational diffusion of a fluctuating quasi‐rigid structure, to analyze nmr spin–lattice relaxation behavior. © 1999 John Wiley & Sons, Inc. Biopoly 49: 235–254, 1999     

Modelling responses of pine savannas to climate change and large‐scale disturbance

Global warming can potentially influence ecological communities through altered disturbance regimes in addition to increased temperatures. We investigate the response of pine savannas in the southeastern United States to global warming using a simple Lotka‐Volterra competition model together with predicted changes to fire and hurricane disturbance regimes with global climate change. In the southeastern United States, decreased frequency of both fires and hurricanes with global warming will shift pine savannas toward a forested state. A CO₂ fertilization effect that increases the growth rate of tree populations will also push southeastern landscapes from open savannas towards closed forests. Transient dynamics associated with climate driven changes in vegetation will last on the order of decades to a century. In our model, the sensitivity of savannas to relative changes in the frequency of fire versus hurricanes is linearly dependent on the growth rate and mortality of trees in fire and hurricane disturbances.     

Solution Conformation of [D-Pen2,D-Pen5]enkephalin in Water: A NMR and Molecular Dynamics Study

The solution conformation of [D -Pen²,D -Pen⁵] enkephalin (DPDPE), a highly potent δ-selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one- and two-dimensional methods of ¹H and ¹³C-NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.     

Nonspecific yet decisive: Ubiquitination can affect the native‐state dynamics of the modified protein

Ubiquitination is one of the most common post‐translational modifications of proteins, and mediates regulated protein degradation among other cellular processes. A fundamental question regarding the mechanism of protein ubiquitination is whether and how ubiquitin affects the biophysical nature of the modified protein. For some systems, it was shown that the position of ubiquitin within the attachment site is quite flexible and ubiquitin does not specifically interact with its substrate. Nevertheless, it was revealed that polyubiquitination can decrease the thermal stability of the modified protein in a site‐specific manner because of alterations of the thermodynamic properties of the folded and unfolded states. In this study, we used detailed atomistic simulations to focus on the molecular effects of ubiquitination on the native structure of the modified protein. As a model, we used Ubc7, which is an E2 enzyme whose in vivo ubiquitination process is well characterized and known to lead to degradation. We found that, despite the lack of specific direct interactions between the ubiquitin moiety and Ubc7, ubiquitination decreases the conformational flexibility of certain regions of the substrate Ubc7 protein, which reduces its entropy and thus destabilizes it. The strongest destabilizing effect was observed for systems in which Lys48‐linked tetra‐ubiquitin was attached to sites used for in vivo degradation. These results reveal how changes in the configurational entropy of the folded state may modulate the stability of the protein's native state. Overall, our results imply that ubiquitination can modify the biophysical properties of the attached protein in the folded state and that, in some proteins, different ubiquitination sites will lead to different biophysical outcomes. We propose that this destabilizing effect of polyubiquitin on the substrate is linked to the functions carried out by the modification, and in particular, regulatory control of protein half‐life through proteasomal degradation.     

Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis

A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak frequencies below 80 cm^?1, and harmonic modes with frequencies above this value. In general the larger the mean-square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean-square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi-dimensional parabola which is just a resealed version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the resealing factor, termed the “normal mode resealing factor,” has apparently converged to a value whereby the mean-square fluctuation within the subspace is about twice that predicted by the normal mode analysis. © 1995 Wiley-Liss, Inc.     

Mutational analysis of FUS gene and its structural and functional role in amyotrophic lateral sclerosis 6

Amyotrophic lateral sclerosis 6 (ALS6) is an autosomal recessive disorder caused by heterozygous mutation in the Fused in Sarcoma (FUS) gene. ALS6 is a neurodegenerative disorder, which affects the upper and lower motor neurons in the brain and spinal cord, resulting in fatal paralysis. ALS6 is caused by the genetic mutation in the proline/tyrosine-nuclear localization signals of the Fused in sarcoma Protein (FUS). FUS gene also known as TLS (Translocated in liposarcoma), which encodes a protein called RNA-binding protein-Fus (FUS), has a molecular weight of 75?kDa. In this analysis, we applied computational approach to filter the most deleterious and neurodegenerative disease of ALS6-associated mutation on FUS protein. We found H517Q as most deleterious and disease associated using PolyPhen 2.0, I-Mutant 3.0, SIFT, SNPs&GO, PhD-SNP, Pmut, and Mutpred tools. Molecular dynamics simulation (MDS) approach was conducted to investigate conformational changes in the mutant protein structure with respect to its native conformation. MDS results showed the flexibility loss in mutant (H517Q) FUS protein. Due to mutation, FUS protein became more rigid in nature and might alter the structural and functional behavior of protein and play a major role in inducing ALS6. The results obtained from this investigation would help in the field of pharmacogenomics to develop a potent drug target against FUS-associated neurodegenerative diseases.     

Triple-resonance NOESY-based experiments with improved spectral resolution: Applications to structural characterization of unfolded, partially folded and folded proteins

NMR-based structural studies of macromolecules focus to a large extent on the establishmentof interproton distances within the molecule based on the nuclear Overhauser effect (NOE).Despite the improvements in resolution resulting from multidimensional NMR experiments,the detailed characterization of disordered states of proteins or highly overlapped regions offolded molecules using current NMR methods remains challenging. A suite of triple-resonanceNOESY-type pulse schemes is presented which require uniform 15N and 13C labeling andmake use of the chemical shift dispersion of backbone 15N and 13C (carbonyl)resonances to increase the spectral resolution. In particular, for the case of partially folded andunfolded proteins, the experiments exploit the fact that the dispersion of 15N and 13Cresonances is comparable to that observed in folded states. Ambiguities that arise in theassignment of NOEs as a result of the severe chemical shift degeneracy in 1H and aliphatic13C nuclei are resolved, therefore, by recording the chemical shifts of 15N or 13Ceither before or after the NOE mixing period. Applications of these methods to the study ofthe unfolded state of the N-terminal SH3 domain of drk (drkN SH3) and a partially foldedlarge fragment of staphylococcal nuclease (SNase), 131, are presented. Inaddition, an application to folded SNase in complex with the ligands thymidine3,5-bisphosphate (pdTp) and Ca2+ is illustrated which allows the assignmentof NOEs between degenerate H protons or protons resonating close to water.     

Cosolvent,ions, and temperature effects on the structural properties of cecropin A‐Magainin 2 hybrid peptide in solutions

Antimicrobial peptides are promising alternative to traditional antibiotics and antitumor drugs for the battle against new antibiotic resistant bacteria strains and cancer maladies. The study of their structural and dynamics properties at physiological conditions can help to understand their stability, delivery mechanisms, and activity in the human body. In this article, we have used molecular dynamics simulations to study the effects of solvent environment, temperature, ions concentration, and peptide concentration on the structural properties of the antimicrobial hybrid peptide Cecropin A–Magainin 2. In TFE/water mixtures, the structure of the peptide retained α‐helix contents and an average hinge angle in close agreement with the experimental NMR and CD measurements reported in literature. Compared to the TFE/water mixture, the peptide simulated at the same ionic concentration lost most of its α‐helix structure. The increase of peptide concentration at both 300 and 310 K resulted in the peptide aggregation. The peptides in the complex retained the initial N‐ter α‐helix segment during all the simulation. The α‐helix stabilization is further enhanced in the high salt concentration simulations. The peptide aggregation was not observed in TFE/water mixture simulations and, the peptide aggregate, obtained from the water simulation, simulated in the same conditions did dissolve within few tens of nanoseconds. The results of this study provide insights at molecular level on the structural and dynamics properties of the CA‐MA peptide at physiological and membrane mimic conditions that can help to better understand its delivery and interaction with biological interfaces. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 1–14, 2015.     

CF3‐Pyridinyl Substitution on Antimalarial Therapeutics: Probing Differential Ligand Binding and Dynamical Inhibitory Effects of a Novel Triazolopyrimidine‐Based Inhibitor on Plasmodium falciparum Dihydroorotate Dehydrogenase

The quest for reliable dihydroorotate dehydrogenase (DHODH) inhibitors has engendered the discovery of potential therapeutic compounds at different stages of clinical trials. Although promising, high attrition rates and unfavorable bioactivities have limited their drug developmental progress. A recent structural modification of DSM265, a triazolopyrimidine‐based inhibitor, yielded DSM421, derived by the substitution of the SF₅‐aniline group on DSM265 with a CF₃‐pyridinyl moiety. Consequently, DSM421 exhibited improved pharmacological and pharmacokinetics attributes relative to DSM265. The improved bioactivity mediated by the CF₃‐pyridinyl group leaves us with a curiosity to investigate underlying ligand‐binding mechanisms and dynamics using computational methods. Presented in this study are insights that clearly explain the effects of structural SF₅‐aniline→CF₃‐pyridinyl modifications on pfDHODH inhibition. Findings showed that the CF₃‐pyridinyl group induced an optimal and stabilized positioning of DSM421 within the binding pocket, allowing for steady and strong intermolecular interactions which favored its stronger binding affinity as estimated and correlated with bioactivity data. These interactions consequently induced a pronounced stabilization of the structural conformation of pfDHODH by restricting residue motions, which possibly underpinned its enhanced inhibitory activity relative to DSM265. Active site interactions of the CF₃‐pyrinidyl group with residues Ser236, Ile237, and Phe188 characterized by strong π–π stacking and halogen interactions also stabilized its positioning which altogether accounted for its enhanced inhibitory prowess towards pfDHODH. On the contrary, fewer and weaker interactions characterized DSM265 binding which could explain its relatively lower binding affinity. Findings will facilitate the design of novel pfDHODH inhibitors with enhanced properties.     

Dynameomics: Data‐driven methods and models for utilizing large‐scale protein structure repositories for improving fragment‐based loop prediction

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment‐based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ～25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root‐mean‐square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments .     

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.

A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.     

The role of disulfide bonds and N‐terminus in the structural properties of hepcidins: Insights from molecular dynamics simulations

The main purpose of this work is to analyse, by means of molecular dynamics (MD) simulations both structural and mechanical‐dynamical differences between Hepcidin‐20 and Hepcidin‐25 in both oxidized and reduced states in aqueous solution. Results indicate that the presence of disulfide bonds is essential, in both peptides, for maintaining their β‐hairpin motif. As a matter of fact, the lack of this intra‐peptide covalent interactions produces an almost immediate deviation from the oxidized, plausibly active, structure in both the systems. Interestingly, reduced Hepcidin‐25 turns out to be characterized by a highly fluctuating structure which is found to rapidly span a large number of configurations at equilibrium. On the other hand, loss of disulfide bonds in the shorter peptide, results in a more compact and relatively rigid double‐turn structure. Comparison of mechanical–dynamical properties and sidechains–sidechains interactions in oxidized Hepcidin‐20 and Hepcidin‐25 strongly suggest also the key role of N‐terminus in the aggregation tendency of Hepcidin‐25. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 917–926, 2010.