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The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growthJun 13 2019Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability of amyloid ... More
Simulated Epidemics in 3D Protein Structures to Detect Functional PropertiesJun 12 2019The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing ideas from ... More
In silico evidence that protein unfolding is as a precursor of the protein aggregationJun 12 2019We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native ... More
High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnetsJun 12 2019State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajectory data. In molecular dynamics simulations, these data-driven collective ... More
Protein contact map prediction using bi-directional recurrent neural networkJun 11 2019Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional methods is generally ... More
Phylogenetic correlations can suffice to infer protein partners from sequencesJun 10 2019Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners among the ... More
Critical phenomena in the temperature-pressure-crowding phase diagram of a proteinJun 09 2019In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural ... More
OnionNet: a multiple-layer inter-molecular contact based convolutional neural network for protein-ligand binding affinity predictionJun 06 2019Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in general. The accuracies ... More
Enhancing the performance of DNA surface-hybridization biosensors through target depletionJun 04 2019DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary ... More
Energy landscapes and dynamics of xylo-nucleic acidsJun 03 2019Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate ... More
Scaffold-based molecular design using graph generative modelMay 31 2019Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a particular scaffold ... More
Current enhancement in solid-state nanopores depends on three-dimensional DNA structureMay 31 2019The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change ... More
Collective-variable selection and generative Hopfield-Potts models for protein-sequence familiesMay 28 2019Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the three-dimensional structure ... More
Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networksMay 28 2019Two types of osmolytes, i.e., trimethylamin N-oxide (TMAO) and urea, demonstrate dramatically different properties in a protein folding process. Even with the great progresses in revealing the potential underlying mechanism of these two osmolyte systems, ... More
Role of Ligand Conformation on Nanoparticle-Protein InteractionsMay 28 2019Engineered biomedical nanoparticles (NP) administered via intravenous routes are prone to associate to serum proteins. The protein corona can mask the NP surface functionalization and hamper the delivery of the NP to its biological target. The design ... More
AmoebaContact and GDFold: a new pipeline for rapid prediction of protein structuresMay 28 2019Native contacts between residues could be predicted from the amino acid sequence of proteins, and the predicted contact information could assist the de novo protein structure prediction. Here, we present a novel pipeline of a residue contact predictor ... More
Towards Interpretable Sparse Graph Representation Learning with Laplacian PoolingMay 28 2019Recent work in graph neural networks (GNNs) has lead to improvements in molecular activity and property prediction tasks. However, GNNs lack interpretability as they fail to capture the relative importance of various molecular substructures due to the ... More
Investigation of HIV-1 Gag binding with RNAs and Lipids using Atomic Force MicroscopyMay 27 2019Atomic Force Microscopy was utilized to study the morphology of Gag, {\Psi}RNA, and their binding complexes with lipids in a solution environment with 0.1{\AA} vertical and 1nm lateral resolution. TARpolyA RNA was used as a RNA control. The lipid used ... More
A COLD Approach to Generating Optimal SamplesMay 23 2019Optimising discrete data for a desired characteristic using gradient-based methods involves projecting the data into a continuous latent space and carrying out optimisation in this space. Carrying out global optimisation is difficult as optimisers are ... More
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsinMay 22 2019Bacteriorhodopsin (bR) is a light-driven proton pump. We use time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast ... More
Molecular rules for selectivity in lipase-catalysed acylation of lysineMay 21 2019The selectivity of L-lysine acylation by lauric acid catalysed by Candida antarctica lipase B (CALB) was investigated combining experimental and theoretical methodologies. Experiments showed the near-exclusive acylation of lysine $\epsilon$-amino group; ... More
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samplesMay 21 2019Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties ... More
ROMEO: A Plug-and-play Software Platform of Robotics-inspired Algorithms for Modeling Biomolecular Structures and MotionsMay 20 2019Motivation: Due to the central role of protein structure in molecular recognition, great computational efforts are devoted to modeling protein structures and motions that mediate structural rearrangements. The size, dimensionality, and non-linearity of ... More
Transient hydrophobic exposure in the molecular dynamics of Abeta peptide at low water concentrationMay 20 2019Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We subjected Abeta40 ... More
Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutionsMay 19 2019RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots ... More
Limitations in Predicting Radiation-Induced Pharmaceutical Instability during Long-Duration SpaceflightMay 15 2019As human spaceflight seeks to expand beyond low-Earth orbit, NASA and its international partners face numerous challenges related to ensuring the safety of their astronauts, including the need to provide a safe and effective pharmacy for long-duration ... More
Size and structure of the sequence space of repeat proteinsMay 11 2019The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be estimated using models ... More
Thermal Fracture Kinetics of Heterogeneous Semiflexible PolymersMay 08 2019The fracture and severing of polymer chains plays a critical role in the failure of fibrous materials and the regulated turnover of intracellular filaments. Using continuum wormlike chain models, we investigate the fracture of semiflexible polymers via ... More
Parameter-free Clustering of Free Energy Landscapes with Gaussian MixturesMay 08 2019Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This ... More
Allostery and conformational changes upon binding as generic features of proteins: a high-dimension geometrical approachMay 07 2019A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon binding. O. ... More
tRNA as stabilizing matrix for fluorescent silver clusters: photophysical properties and IR studyMay 04 2019In this experimental study fluorescent silver clusters on tRNA matrix were synthesized for the first time. Obtained complexes have two emission regions in visible part of spectrum. We have also studied our complexes using FTIR spectroscopy. The possible ... More
tRNA as stabilizing matrix for fluorescent silver clusters: photophysical properties and IR studyMay 04 2019May 18 2019In this experimental study fluorescent silver clusters on tRNA matrix were synthesized for the first time. Obtained complexes have two emission regions in visible part of spectrum. We have also studied our complexes using FTIR spectroscopy. The possible ... More
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its Sequence -Structure -Function analysisMay 02 2019Background. Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. More than 800 different sequences have been characterized so far, but their biological functions remain ... More
DNA energy constraints shape biological evolutionary trajectoriesMay 02 2019Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetrate themselves. Thus, the biological information contained within a dsDNA molecule, in terms of a linear sequence of nucleotides, has been considered ... More
Machine Learning for Classification of Protein Helix Capping MotifsMay 01 2019The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the sequence, defines ... More
A polymer model of bacterial supercoiled DNA including structural transitions of the double helixApr 25 2019DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures ... More
Topology, Landscapes, and Biomolecular Energy TransportApr 25 2019While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes conspire to produce behavior ... More
Backbone chemical shift assignments of human 14-3-3$σ$Apr 24 201914-3-3 proteins are a group of seven dimeric adapter proteins that exert their biological function by interacting with hundreds of phosphorylated proteins, thus influencing their sub-cellular localization, activity or stability in the cell. Due to this ... More
The lubricity of mucin solutions is robust against changes in physiological conditionsApr 18 2019Solutions of manually purified gastric mucins have been shown to be promising lubricants for biomedical purposes, where they can efficiently reduce friction and wear. However, so far, such mucin solutions have been mostly tested in specific settings, ... More
DeepNovoV2: Better de novo peptide sequencing with deep learningApr 17 2019May 22 2019Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising ... More
DeepNovoV2: Better de novo peptide sequencing with deep learningApr 17 2019We introduce DeepNovoV2, the state-of-the-art neural networks based model for de novo peptide sequencing. Contrary to existing models like DeepNovo or DeepMatch which represents each spectrum as a long sparse vector, in DeepNovoV2, we propose to directly ... More
Cryo-Electron Microscopy Image Analysis Using Multi-Frequency Vector Diffusion MapsApr 16 2019Cryo-electron microscopy (EM) single particle reconstruction is an entirely general technique for 3D structure determination of macromolecular complexes. However, because the images are taken at low electron dose, it is extremely hard to visualize the ... More
Detection of protein-ligand binding sites with 3D segmentationApr 13 2019In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural networks especially, ... More
Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure predictionApr 13 2019Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement experimental efforts by ... More
Molecular simulations have boosted knowledge of CRISPR/Cas9: A ReviewApr 12 2019Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic acid complexes. ... More
Partial covariance two-dimensional mass spectrometry for determination of biomolecular primary structureApr 11 2019Mass spectrometry (MS) is used widely in biomolecular structural analysis and is particularly dominant in the study of proteins. Despite its considerable power, state-of-the-art protein MS frequently suffers from limited reliability of spectrum-to-structure ... More
Repurposing of Ring Framework through TR screeningApr 11 2019In the drug repurposing approach, the chemically diverse and potentially safe molecules can be explored as therapeutic potential out of those originally targeted indications. However, the intellectual property rights, and competitive over-heating issue ... More
Crowding-induced Elongated Conformation of Urea-unfolded Apoazurin: Investigating the Role of Crowder Shape In SilicoApr 09 2019Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect ... More
Twist-bend coupling, twist waves and DNA loopsApr 09 2019In vivo, DNA forms loops over a broad range of length scales: from several thousand base pairs (bp) down to about 100 bp. In loops shorter than the DNA persistence length (150 bp), thermal fluctuations can be neglected, and the molecule assumes approximately ... More
Globular bundles and entangled network of proteins (CorA) by a coarse-grained Monte Carlo simulationApr 09 2019Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein concentration at a ... More
Conformational catalysis of cataract-associated aggregation by interacting intermediates in a human eye lens crystallinApr 07 2019Most known proteins in nature consist of multiple domains. Interactions between domains may lead to unexpected folding and misfolding phenomena. This study of human {\gamma}D-crystallin, a two-domain protein in the eye lens, revealed one such surprise: ... More
Global Small-Angle Scattering Data Analysis of Inverted Hexagonal PhasesApr 05 2019We have developed a global analysis model for randomly oriented, fully hydrated inverted hexagonal (H$_\text{II}$) phases formed by many amphiphiles in aqueous solution, including membrane lipids. The model is based on a structure factor for hexagonally ... More
The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNAApr 04 2019The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have physiological relevance ... More
PyRod - Tracing water molecules in molecular dynamics simulationsApr 03 2019Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the drug design ... More
BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting ModelApr 02 2019RNA-RNA interaction (RRI) is ubiquitous and has complex roles in the cellular functions. In human health studies, miRNA-target and lncRNAs are among an elite class of RRIs that have been extensively studied. Bacterial ncRNA-target and RNA interference ... More
Strand displacement: a fundamental mechanism in RNA biology?Mar 28 2019DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures with predefined ... More
Bio-energy Transport as a Phonon Dressed Vibrational Exciton in Protein MoleculesMar 27 2019Following the ideas of Davydov's soliton theory, we study the bio-energy transport in protein molecules. By using a quantum Brownian motion model for a phonon dressed vibrational exciton, we calculate the time-dependence on the mean square distance, diffusion ... More
PCL enzymatic hydrolysis: a mechanistic studyMar 27 2019Accumulation of plastic waste is a major environmental problem. Enzymes, particularly esterases, play an important role in the biodegradation of polyesters. These enzymes are usually only active on aliphatic polyesters, but a few have showed catalytic ... More
Atom-specific persistent homology and its application to protein flexibility analysisMar 26 2019Recently, persistent homology has had tremendous success in biomolecular data analysis. It works by examining the topological relationship or connectivity of a group of atoms in a molecule at a variety of scales, then rendering a family of topological ... More
Angiotensin II cyclic analogs as tools to investigate AT1R biased signaling mechanismsMar 26 2019G protein coupled receptors (GPCRs) produce pleiotropic effects by their capacity to engage numerous signaling pathways once activated. Functional selectivity (also called biased signaling), where specific compounds can bring GPCRs to adopt conformations ... More
BpForms: a toolkit for concretely describing modified DNA, RNA and proteinsMar 24 2019Summary: Non-canonical nucleic and amino acid monomers are essential to enhance the information capacity, functional capabilities, and stability of DNA, RNA, and protein biopolymers. However, there are few tools for describing the primary structure of ... More
Stimulated Binding of Polymer Chains by Narrow Tube ConfinementMar 19 2019In biology, there are several processes in which unfolded protein chains are transported along narrow tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However, when chain entropy ... More
Stimulated Binding of Polymer Chains by Narrow Tube ConfinementMar 19 2019Apr 02 2019In biology, there are several processes in which unfolded protein chains are transported along narrow tube channels. Normally, without such a severe configurational constraint, unfolded polypeptides would not bind to each other. However, when chain entropy ... More
Principal component analysis of nonequilibrium molecular dynamics simulationsMar 19 2019Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system. While PCA is routinely ... More
Principal component analysis of nonequilibrium molecular dynamics simulationsMar 19 2019May 29 2019Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system. While PCA is routinely ... More
Principal component analysis of nonequilibrium molecular dynamics simulationsMar 19 2019May 02 2019Principal component analysis (PCA) represents a standard approach to identify collective variables $\{x_i\}\!=\!\boldsymbol{x}$, which can be used to construct the free energy landscape $\Delta G(\boldsymbol{x})$ of a molecular system. While PCA is routinely ... More
The limited roles of autocatalysis and enantiomeric cross inhibition in achieving homochirality in dilute systemsMar 19 2019To understand the effects of fluctuations on achieving homochirality, we employ a Monte-Carlo method where autocatalysis and enantiomeric cross-inhibition, as well as racemization and deracemization reactions are included. The results of earlier work ... More
Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variantMar 18 2019AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type, is caused by pathological aggregation of proteolytic fragments of plasma gelsolin. So far, four mutations in the gelsolin gene have been reported as responsible for the disease. ... More
Mechanics and Structural Stability of the Collagen Triple HelixMar 18 2019The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing biological pathways ... More
Review on DNA CryptographyMar 15 2019Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality, integrity and availability ... More
More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018Mar 14 2019We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the ... More
Topological Indices of ProteinsMar 11 2019Protein molecules can be approximated by discrete polygonal chains of amino acids. Standard topological tools can be applied to the smoothening of the polygons to introduce a topological classification of proteins, for example, using the self-linking ... More
Robust Inference of Forces in Heterogeneous EnvironmentsMar 07 2019We devise a method to obtain a robust estimate of forces in a heterogeneous environment based on experimentally recorded trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed force ... More
Weighted persistent homology for biomolecular data analysisMar 07 2019In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices ... More
Review on DNA Strand Algebra and its ApplicationMar 04 2019Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades, DNA computing ... More
Electronic Spectroscopy of Isolated DNA PolyanionsFeb 28 2019In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could ... More
Universality of fold-encoded localized vibrations in enzymesFeb 26 2019Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, ... More
Multiple Scales in the Simulation of Ion Channels and ProteinsFeb 24 2019Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists see a structure, ... More
Multiple Scales in the Simulation of Ion Channels and ProteinsFeb 24 2019Mar 04 2019Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists see a structure, ... More
Learning protein sequence embeddings using information from structureFeb 22 2019Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. ... More
Machine-Learning-Assisted Directed Protein Evolution with Combinatorial LibrariesFeb 19 2019To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow. Combinatorial sequence ... More
Machine learning-assisted directed protein evolution with combinatorial librariesFeb 19 2019May 22 2019To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow. Combinatorial sequence ... More
Machine-Learning-Assisted Directed Protein Evolution with Combinatorial LibrariesFeb 19 2019Feb 21 2019To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow. Combinatorial sequence ... More
The Essential Role of Thermodynamics in metabolic network modeling: physical insights and computational challengesFeb 19 2019Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge ... More
Evolutionary dynamics determines adaptation to inactivation of an essential geneFeb 18 2019Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing ... More
Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice ProteinsFeb 18 2019A Restricted Boltzmann Machine (RBM) is an unsupervised machine-learning bipartite graphical model that jointly learns a probability distribution over data and extracts their relevant statistical features. As such, RBM were recently proposed for characterizing ... More
Formation of native shortcut networks and two-state protein foldingFeb 17 2019Mar 19 2019A dynamic network-centric approach to study two-state folding from native structure called network dynamics (ND) is introduced. ND applies two fundamental principles of protein folding: hydrophobicity and loop-entropy, on a protein's native residue network ... More
Formation of native shortcut networks and two-state protein foldingFeb 17 2019A dynamic network-centric approach to study two-state folding from native structure called network dynamics (ND) is introduced. ND applies two fundamental principles of protein folding: hydrophobicity and loop-entropy, on a protein's native residue network ... More
Ion Condensation onto Ribozyme is Site-Specific and Fold-DependentFeb 15 2019The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more efficient than ... More
Ion Condensation onto Ribozyme is Site-Specific and Fold-DependentFeb 15 2019Apr 13 2019The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more efficient than ... More
Circular spectropolarimetric sensing of vegetation in the field; possibilities for the remote detection of extraterrestrial lifeFeb 15 2019Homochirality is a generic and unique property of all biochemical life and the fractional circular polarization it induces therefore constitutes an unambiguous biosignature. However, while high-quality circular polarimetric spectra can be easily and quickly ... More
Thermodynamics of force-induced B-DNA melting: single-strand discreteness mattersFeb 15 2019Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced ... More
Use Symmetry to Elucidate the Roles of Global Shape and Local Interactions in Protein Dynamics and CooperativityFeb 10 2019Shape had been intuitively recognized to play a dominant role in determining the global motion patterns of bio-molecular assemblies. However, it is not clear exactly how shape determines the motion patterns. What about the local interactions that hold ... More
Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised Deep LearningFeb 09 2019Unsupervised clustering has broad applications in data stratification, pattern investigation and new discovery beyond existing knowledge. In particular, clustering of bioactive molecules facilitates chemical space mapping, structure-activity studies, ... More
How superlocalization affects Vibrational Energy Exchange process in proteinsFeb 08 2019May 12 2019Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a theoretical picture, ... More
Fractal nature of protein structures affects their Vibrational Energy ExchangeFeb 08 2019Recent vibrational energy exchange experiments on a protein have been explained employing the relation, not new in itself, between protein and fractal structure. The differnce in the scaling exponent of specific part of the protein entails a distinct ... More
MENSADB: A Thorough Structural Analysis of Membrane Protein DimersFeb 06 2019Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance, respiration, ... More
Efficient conversion of chemical energy into mechanical work by Hsp70 chaperonesFeb 05 2019Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical approaches to elucidate ... More
Efficient conversion of chemical energy into mechanical work by Hsp70 chaperonesFeb 05 2019Mar 29 2019Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here we combine complementary computational/theoretical approaches to elucidate ... More
Observing monomer - dimer transitions of neurotensin receptors 1 in single SMALPs by homoFRET and in an ABELtrapFeb 05 2019G protein-coupled receptors (GPCRs) are a large superfamily of membrane proteins that are activated by extracellular small molecules or photons. Neurotensin receptor 1 (NTSR1) is a GPCR that is activated by neurotensin, i.e. a 13 amino acid peptide. Binding ... More