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mGPfusion: Predicting protein stability changes with Gaussian process kernel learning and data fusionFeb 08 2018Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary ... More
Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug MetforminFeb 07 2018Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows anti-tumour activities ... More
Automatic microtubule tracking in fluorescence images of cells doped with increasing concentrations of taxol and nocodazoleFeb 05 2018The purpose of this paper is to provide an algorithm for detecting and tracking astral MTs in a fully automated way and supply a description of their dynamic behaviour. For the algorithm testing, a dataset of stacks (i.e. time-lapse image sequences), ... More
A digital microarray using interferometric detection of plasmonic nanorod labelsJan 23 2018DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and dynamic range of traditional fluorescence microarrays compared ... More
Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptidesJan 15 2018We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained ... More
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulationsDec 21 2017Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain statistically ... More
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifsNov 02 2017Dec 06 2017We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic ... More
Designing RNA Secondary Structures is HardOct 31 2017An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can be represented ... More
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular DynamicsSep 25 2017Dec 14 2017Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential degrees of freedom ... More
An infinite class of unsaturated rooted trees corresponding to designable RNA secondary structuresSep 23 2017Jan 17 2018An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to determine whether ... More
Multiple scales and phases in discrete chains with application to folded proteinsMay 26 2017Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape. Multiple scales ... More
Effect of Surfaces on Amyloid Fibril FormationApr 26 2017Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid with cell ... More
Experimental measurement of binding energy, selectivity and allostery using fluctuation theoremsMar 30 2017Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, ... More
Protein-Ligand Scoring with Convolutional Neural NetworksDec 08 2016Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict binding affinities ... More
A review of geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular dataDec 06 2016Geometric, topological and graph theory modeling and analysis of biomolecules are of essential importance in the conceptualization of molecular structure, function, dynamics, and transport. On the one hand, geometric modeling provides molecular surface ... More
A Graph Grammar for Modelling RNA FoldingDec 06 2016We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour ... More
Towards multistage modelling of protein dynamics with monomeric Myc oncoprotein as an exampleDec 05 2016We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate an isolated ... More
Finding the minimum energy conformation of protein-like heteropolymers by Greedy Neighborhood SearchDec 03 2016A global optimization method called Greedy Neighborhood Search (GNS) and a novel conformational sampling method using a spherical distribution is proposed to find the minimum energy conformation of a protein-like heteropolymer model called AB model. The ... More
How to measure the topological quality of protein grammars?Nov 30 2016Context-free and context-sensitive formal grammars are often regarded as more appropriate to model proteins than regular level models such as finite state automata and Hidden Markov Models. In theory, the claim is well founded in the fact that many biologically ... More
Lipidomic approach for stratification of Acute Myeloid Leukemia patientsNov 30 2016The pathogenesis and progression of many tumors, including hematologic malignancies is highly dependent on enhanced lipogenesis. De novo fatty-acid synthesis permits accelerated proliferation of tumor cells by providing structural components to build ... More
PeBLes: Prediction of B-cell epitope using molecular layersNov 29 2016Characterization of B-cell protein epitope and developing critical parameters for its identification is one of the long standing interests. Using Layers algorithm, we introduced the concept of anchor residues to identify epitope. We have shown that majority ... More
Tip-enhanced Raman spectroscopic detection of aptamersNov 29 2016Single molecule detection, sequencing and conformational mapping of aptamers are important for improving medical and biosensing technologies and for better understanding of biological processes at the molecular level. We obtain vibrational signals of ... More
Graph's Topology and Free Energy of a Spin Model on the GraphNov 29 2016In this work we show that there is a direct relationship between a graph's topology and the free energy of a spin system on the graph. We develop a method of separating topological and enthalpic contributions to the free energy, and find that considering ... More
Thermodynamic competition between membrane protein oligomeric statesNov 28 2016Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical framework describing ... More
Solution X-ray scattering (S/WAXS) and structure formation in protein dynamicsNov 24 2016We propose to develop mean field theory in combination with Glauber algorithm, to model and interpret protein dynamics and structure formation in small to wide angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analysing the Engrailed ... More
Specificity-determining DNA triplet code for positioning of human pre-initiation complexNov 23 2016The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. In a pioneering study by Pugh and Venters no specific consensus motif for the positioning of the human pre-initiation complex (PIC) ... More
3D Reconstruction of Heterogeneous Virus Particles with Statistical Geometric SymmetryNov 21 2016In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry, it is natural ... More
Proteins analysed as virtual knotsNov 18 2016Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear ... More
Combining simulations and solution experiments as a paradigm for RNA force field refinementNov 18 2016Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with ... More
Variants of intrinsic disorder in the human proteomeNov 18 2016In this paper we propose a straightforward operational definition of variants of disordered proteins, taking the human proteome as a case study. The focus is on a distinction between mostly unstructured proteins and proteins which contain long unstructured ... More
Benchmarking inverse statistical approaches for protein structure and design with exactly solvable modelsNov 15 2016Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the inferred effective ... More
Electrostatic Forces Mediate Fast Association of Calmodulin and the Intrinsically Disordered Regulatory Domain of CalcineurinNov 13 2016Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) govern a daunting number of physiological processes. For such proteins, molecular mechanisms governing their interactions with proteins involved in signal ... More
High-Resolution Structure and Intermolecular Interactions between L-type Straight Flagellar FilamentsNov 12 2016Bacterial mobility is powered by rotation of helical flagellar filaments driven by rotary motors. Flagellin isolated from {\it Salmonella Typhimurium} SJW1660 strain, which differs by a point mutation from the wild-type strain, assembles into straight ... More
Mahalanobis Distance for Class Averaging of Cryo-EM ImagesNov 10 2016Nov 12 2016Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing ... More
Mahalanobis Distance for Class Averaging of Cryo-EM ImagesNov 10 2016Nov 18 2016Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing ... More
Mahalanobis Distance for Class Averaging of Cryo-EM ImagesNov 10 2016Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at unknown viewing ... More
Small-angle scattering studies of intrinsically disordered proteins and their complexesNov 07 2016Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the conformational plasticity ... More
Protein Secondary Structure Prediction Using Deep Multi-scale Convolutional Neural Networks and Next-Step ConditioningNov 04 2016Recently developed deep learning techniques have significantly improved the accuracy of various speech and image recognition systems. In this paper we adapt some of these techniques for protein secondary structure prediction. We first train a series of ... More
RBPBind: Quantitative prediction of Protein-RNA InteractionsNov 04 2016Summary: We introduce RBPBind, a web-based tool for the quantitative prediction of RNA-protein interactions. Given a user-specified RNA and a protein selected from a set of several common RNA-binding proteins, RBPBind computes the binding curve and effective ... More
Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface ConditionNov 03 2016We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in water--co-solvent mixtures. ... More
Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface ConditionNov 03 2016Nov 15 2016We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in water--co-solvent mixtures. ... More
Symmetry and size of membrane protein polyhedral nanoparticlesNov 02 2016In recent experiments [T. Basta et al., Proc. Natl. Acad. Sci. U.S.A. 111, 670 (2014)] lipids and membrane proteins were observed to self-assemble into membrane protein polyhedral nanoparticles (MPPNs) with a well-defined polyhedral protein arrangement ... More
Bilayer-thickness-mediated interactions between integral membrane proteinsNov 02 2016Hydrophobic thickness mismatch between integral membrane proteins and the surrounding lipid bilayer can produce lipid bilayer thickness deformations. Experiment and theory have shown that protein-induced lipid bilayer thickness deformations can yield ... More
Architecture and Function of Mechanosensitive Membrane Protein LatticesNov 02 2016Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular ... More
Signatures of protein structure in the cooperative gating of mechanosensitive ion channelsNov 02 2016Membrane proteins deform the surrounding lipid bilayer, which can lead to membrane-mediated interactions between neighboring proteins. Using the mechanosensitive channel of large conductance (MscL) as a model system, we demonstrate how the observed differences ... More
A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding siteNov 02 2016In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the ... More
Folding with a protein's native shortcut networkNov 01 2016The physical basis of shortcut edges in a Protein Residue Network (PRN) and their applicability to a simplified protein folding pathway problem is investigated. The results show promise, and suggest the dominant influence of native-state topology even ... More
Variational Methods for Biomolecular ModelingOct 31 2016Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of ... More
All-atom Molecular Dynamics Simulations of the Projection Domain of the Intrinsically Disordered htau40 ProteinOct 30 2016We have performed all atom molecular dynamics simulations on the projection domain of the intrinsically disordered htau40 protein. After generating a suitable ensemble of starting conformations at high temperatures, at room temperature in an adaptive ... More
Stochastic single-molecule dynamics of synaptic membrane protein domainsOct 29 2016Nov 07 2016Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic ... More
Stochastic single-molecule dynamics of synaptic membrane protein domainsOct 29 2016Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic ... More
Supporting novel biomedical research via multilayer collaboration networksOct 28 2016The value of research containing novel combinations of molecules can be seen in many innovative and award-winning research programs. Despite calls to use innovative approaches to address common diseases, an increasing majority of research funding goes ... More
A single step protein assay that is both detergent and reducer compatible: The cydex blue assayOct 24 2016Determination of protein concentration in often an absolute pre-requisite in preparing samples for biochemical and proteomic analyses. However, current protein assay methods are not compatible with both reducers and detergents, which are however present ... More
Maximum-likelihood, self-consistent side chain free energies with applications to protein molecular dynamicsOct 24 2016To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics, we propose a new methodology that computes a self-consistent approximation of the side chain free energy ... More
Variational approximation of molecular kinetics from short off-equilibrium simulationsOct 20 2016Markov state models (MSMs) and Master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, ... More
Theory on the mechanisms of combinatorial binding of transcription factors with DNAOct 20 2016We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated recruitment pathways. ... More
How to fold intricately: using theory and experiments to unravel the properties of knotted proteinsOct 18 2016Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, ... More
Tomographic docking suggests the mechanism of auxin receptor TIR1 selectivityOct 18 2016We study the binding of plant hormone IAA on its receptor TIR1 introducing a novel computational method that we call tomographic docking and that accounts for interactions occurring along the depth of the binding pocket. Our results suggest that selectivity ... More
Stochastic switching between multistable oscillation patterns of the Min-systemOct 17 2016The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the reaction volume, ... More
ProQ3D: Improved model quality assessments using Deep LearningOct 17 2016Summary: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased ... More
ProQ3D: Improved model quality assessments using Deep LearningOct 17 2016Oct 18 2016Summary: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation has increased ... More
A singular mutation in the hemagglutinin of the 1918 pandemic virusOct 14 2016The influenza pandemic of 1918-1919 killed at least 50 million people. The reasons why this pandemic was so deadly remain largely unknown. However, It has been shown that the 1918 viral hemagglutinin allows to reproduce the hallmarks of the illness observed ... More
The Pattern Recognition of Probability Distributions of Amino acids in protein familiesOct 13 2016A pattern Recognition of a probability distribution of amino acids is obtained for selected families of proteins. The mathematical model is derived from a theory of protein families formation which is derived from application of a Pauli's master equation ... More
Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteinsOct 13 2016Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to toxicity. However, ... More
Ionic channels in biological membranes. Electrostatic analysis of a natural nanotubeOct 13 2016Oct 14 2016A simple theory of ion permeation through a channel is presented, in which diffusion occurs according to Fick's law and drift according to Ohm's law, in the electric field determined by all the charges present. This theory accounts for permeation in the ... More
Finding dominant transition pathways via global optimization of actionOct 09 2016Oct 12 2016We present a new computational approach, Action-CSA, to sample multiple reaction pathways with fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing method. This approach successfully ... More
Kinetics of spontaneous filament nucleation via oligomers: insights from theory and simulationOct 07 2016Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that ... More
Understanding the role of transport velocity in biomotor-powered microtubule spool assemblyOct 06 2016We examined the sensitivity of microtubule spools to transport velocity. Perhaps surprisingly, we determined that the steady-state number and size of spools remained constant over a seven-fold range of velocities. Our data on the kinetics of spool assembly ... More
Global analysis of VHHs framework regions with a structural alphabetOct 05 2016The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their ... More
Tuning Multiple Motor Travel Via Single Motor VelocityOct 04 2016Microtubule-based molecular motors often work in small groups to transport cargos in cells. A key question in understanding transport (and its regulation in vivo) is to identify the sensitivity of multiple-motor-based motion to various single molecule ... More
Interplay between velocity and travel distance of kinesin-based transport in the presence of tauOct 04 2016Although the disease-relevant microtubule-associated protein tau is known to severely inhibit kinesin-based transport in vitro, the potential mechanisms for reversing this detrimental effect to maintain healthy transport in cells remain unknown. Here ... More
Microtubule Defects Influence Kinesin-Based Transport In VitroOct 04 2016Microtubules are protein polymers that form "molecular highways" for long-range transport within living cells. Molecular motors actively step along microtubules to shuttle cellular materials between the nucleus and the cell periphery; this transport is ... More
Quantitative Determination of the Probability of Multiple-Motor Transport in Bead-Based AssaysOct 04 2016With their longest dimension typically being less than 100 nm, molecular motors are significantly below the optical-resolution limit. Despite substantial advances in fluorescence-based imaging methodologies, labeling with beads remains critical for optical-trapping-based ... More
Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid AssemblyOct 03 2016Most of the existing research in assembly pathway prediction/analysis of virus cap- sids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This ... More
Rapid solution of the cryo-EM reconstruction problem by frequency marchingOct 03 2016Determining the three-dimensional structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using "single particle" cryo-electron microscopy (cryo-EM) ... More
Amino acid preference against beta sheet through allowing backbone hydration enabled by the presence of cationOct 03 2016It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum Molecular Dynamics, ... More
FRETtranslator: translating FRET traces into RNA structural pathwaysOct 02 2016Recent genome and transcriptome sequencing projects have unveiled a plethora of highly structured RNA molecules as central mediators of cellular function. Single molecule Forster Resonance Energy Transfer (smFRET) is a powerful tool for analyzing the ... More
Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-mimetic, Elastin-like Fusion ProteinOct 02 2016Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally self-assembling supramolecular ... More
Cooperative Protofilament Switching Emerges from Inter-Motor Interference in Multiple-Motor TransportOct 01 2016Within living cells, the transport of cargo is accomplished by groups of molecular motors. Such collective transport could utilize mechanisms which emerge from inter-motor interactions in ways that are yet to be fully understood. Here we combined experimental ... More
Intra-chain organisation of hydrophobic residues controls inter-chain aggregation rates of amphiphilic polymersOct 01 2016Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional biological machinery ... More
A Simple Experimental Model to Investigate Force Range for Membrane Nanotube FormationOct 01 2016The presence of membrane tubules in living cells is essential to many biological processes. In cells, one mechanism to form nanosized lipid tubules is via molecular motor induced bilayer extraction. In this paper, we describe a simple experimental model ... More
A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4Sep 30 2016In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We investigated the use of accelerated simulations to inform on compound design ... More
A Review of Mathematical Modeling, Simulation and Analysis of Membrane Channel Charge TransportSep 29 2016The molecular mechanism of ion channel gating and substrate modulation is elusive for many voltage gated ion channels, such as eukaryotic sodium ones. The understanding of channel functions is a pressing issue in molecular biophysics and biology. Mathematical ... More
Computer Folding of RNA Tetraloops: Identification of Key Force Field DeficienciesSep 27 2016The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. ... More
Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteinsSep 26 2016Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the living cell. ... More
Universal bound on the efficiency of molecular motorsSep 26 2016The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a molecular motor running ... More
Free Energy Landscape of GAGA and UUCG RNA TetraloopsSep 26 2016We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered ... More
In vivo compaction dynamics of bacterial DNA: A fingerprint of DNA/RNA demixing ?Sep 26 2016The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the cell volume. ... More
MOLS 2.0: Software Package for Peptide Modelling and Protein-Ligand DockingSep 24 2016Here we give a detailed description of MOLS 2.0.The source code and binary of MOLS 2.0 are distributed free (under GNU Lesser General Public License) for the scientific community. They are freely available for download at ... More
Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8ASep 22 2016Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions ... More
Protein-protein docking by generalized Fourier transforms on 5D rotational manifoldsSep 21 2016Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either the translational ... More
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy imagesSep 21 2016In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM (BioEM) formalism. ... More
How to distinguish conformational selection and induced fit based on chemical relaxation ratesSep 20 2016Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational transition rates ... More
Ripping RNA by Force using Gaussian Network ModelsSep 17 2016Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context ... More
Generalized flexibility-rigidity indexSep 14 2016Flexibility-rigidity index (FRI) has been developed as a robust, accurate and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility ... More
Bayesian Model Averaging for Ensemble-Based Estimates of Solvation Free EnergiesSep 12 2016This paper applies the Bayesian Model Averaging (BMA) statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range methods for predicting solvation free energies, ranging from empirical statistical models to ... More
Effect of Nanodiamond surfaces on Drug Delivery SystemsSep 09 2016The prospect of RNA nanotechnology is increasing because of its numerous potential applications especially in medical science. The spherical Nanodiamonds (NDs) are becoming popular because of their lesser toxicity, desirable mechanical, optical properties, ... More
Not All Fluctuations are Created Equal: Spontaneous Variations in Thermodynamic FunctionSep 08 2016Almost all processes -- highly correlated, weakly correlated, or correlated not at all---exhibit statistical fluctuations. Often physical laws, such as the Second Law of Thermodynamics, address only typical realizations -- as highlighted by Shannon's ... More
The allostery landscape: quantifying thermodynamic couplings in biomolecular systemsSep 07 2016Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables ... More
Statistical Mechanics and Kinetics of Amyloid FibrillationSep 06 2016Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this ... More