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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
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
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
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
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 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 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
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
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
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
Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolutionFeb 04 2019Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend much on several ... More
Evolving methods for rational de novo design of functional RNA moleculesFeb 04 2019Artificial RNA molecules with novel functionality have many applications in synthentic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient alternative to ... More
GA-Novo: De Novo Peptide Sequencing via Tandem Mass Spectrometry using Genetic AlgorithmFeb 03 2019Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and assign the resulting ... More
Bayesian active learning for optimization and uncertainty quantification in protein dockingJan 31 2019Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification ... More
Ligand-induced oligomerization of the human GPCR neurotensin receptor 1 monitored in living HEK293T cellsJan 31 2019The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that can be expressed in HEK293T cells by stable transfection. Its ligand is a 13-amino-acid peptide that binds with nanomolar affinity from the extracellular side to NTSR1. Ligand ... More
A practical guide to the simultaneous determination of protein structure and dynamics using metainferenceJan 23 2019Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system ... More
Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?Jan 21 2019We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer, and for clarity ... More
Machine-learning a virus assembly fitness landscapeJan 13 2019Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole genome/phenotype ... More
A Martini coarse-grained model of the calcein fluorescent dyeJan 10 2019Calcein leakage assays are a standard experimental set-up for probing the extent of damage induced by external agents on synthetic lipid vesicles. The fluorescence signal associated with calcein release from liposomes is the signature of vesicle disruption, ... More
Pearl-Necklace-Like Local Ordering Drives Polypeptide CollapseJan 10 2019Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects ... More
Involvement of Surfactant Protein D in Ebola Virus Infection Enhancement via Glycoprotein InteractionJan 09 2019Since the largest 2014-2016 Ebola virus disease outbreak in West Africa, understanding of Ebola virus infection has improved, notably the involvement of innate immune mediators. Amongst them, collectins are important players in the antiviral innate immune ... More
Estimation of Distribution Algorithm for Protein Structure PredictionJan 04 2019Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships between protein ... More
Physical Folding Codes for ProteinsJan 04 2019Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded proteins fold reproducibly ... More
A deep learning approach to the structural analysis of proteinsJan 03 2019Deep Learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in which DL-based ... More
Base-pair mismatch can destabilize small DNA loops through cooperative kinkingJan 02 2019Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of tightly bent ... More
Geometric constraints in protein foldingDec 23 2018The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical ... More
Determinants of cyclization-decyclization kinetics of short DNA with sticky endsDec 21 2018Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (< 150 bp) has a strong length dependence, but how it depends on the rotational positioning of the ... More
Algebraic graph learning of protein-ligand binding affinityDec 20 2018Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative approaches. ... More
Substrate inhibition imposes fitness penalty at high protein stabilityDec 18 2018Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which no experimental ... More
Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulationDec 17 2018p27$^{Kip1}$ (p27) is an intrinsically disordered protein (IDP) that folds upon binding to cyclin-dependent kinase (Cdk)$/$cyclin complexes (e.g., Cdk2$/$cyclin A), inhibiting their catalytic activity and causing cell cycle arrest. However, cell division ... More
Resolving dynamics and function of transient states in single enzyme moleculesDec 17 2018We used a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action. By unraveling the kinetic and dynamic interplay of the conformational states, we sought to elucidate the dynamic structural biology of T4L. In particular, by combining ... More
Machine learning-assisted discovery of GPCR bioactive ligandsDec 16 2018While G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Due to the involvement of GPCRs in various signaling pathways and physiological ... More
Properties of a Two Dimensional Model of RNA FoldingDec 15 2018Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P (hydrophobic-hydrophilic) ... More
Localization of Energetic Frustration in ProteinsDec 14 2018We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic ... More
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular MachinesDec 12 2018Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF models galvanized ... More
FoldingZero: Protein Folding from Scratch in Hydrophobic-Polar ModelDec 03 2018De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables thorough investigation ... More
Monomer-induced customisation of UV-cured atelocollagen hydrogel networksDec 03 2018Dec 13 2018The covalent functionalisation of type I atelocollagen with either 4-vinylbenzyl or methacrylamide residues is presented as a simple synthetic strategy to achieve customisable, cell-friendly UV-cured hydrogel networks with widespread clinical applicability. ... More
Identification of kinetic order parameters for non-equilibrium dynamicsNov 30 2018A popular approach to analyze the dynamics of high-dimensional many-body systems, such as macromolecules, is to project the trajectories onto a space of slowly-varying collective variables, where subsequent analyses are made, such as clustering or estimation ... More
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state modelsNov 29 2018The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its ... More
Variational Selection of Features for Molecular KineticsNov 28 2018The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated toolkit for ... More
Machine learning in protein engineeringNov 27 2018Machine learning-guided protein engineering is a new paradigm that enables the optimization of complex protein functions. Machine-learning methods use data to predict protein function without requiring a detailed model of the underlying physics or biological ... More
TorchProteinLibrary: A computationally efficient, differentiable representation of protein structureNov 23 2018Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year saw the emergence ... More
Prediction of Cytochrome P450-Mediated Metabolism Using a Combination of QSAR Derived Reactivity and Induced Fit DockingNov 23 2018Prediction of metabolism in cytochrome P450s remains to be a crucial yet challenging topic in discovering and designing drugs, agrochemicals and nutritional supplements. The problem is challenging because the rate of P450 metabolism depends upon both ... More
GuacaMol: Benchmarking Models for De Novo Molecular DesignNov 22 2018Feb 26 2019De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks ... More
Active dynamics and spatially coherent motion in chromosomes subject to enzymatic force dipolesNov 22 2018Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer and when bound ... More
Formic Acid Decomposition Using Synthesized Ag/TiO2 Nanocomposite in Ethanol-Water Media Under Illumination of Near UV LightNov 22 2018The effect of ethanol-water media on the synthesis of Ag/TiO2 nanocomposite was investigated with 0.05, 0.1 and 0.5 (wt.%) of Ag content. Ethanol was used as hole-scavenger enhancing the photodecomposition of Ag+ ions under illumination of near-UV light. ... More
Guessing the upper bound free-energy difference between native-like structuresNov 21 2018Use of a combination of statistical thermodynamics and the Gershgorin theorem enable us to guess, in the thermodynamic limit, a plausible value for the upper bound free-energy difference between native-like structures of monomeric globular proteins. Support ... More
Direct Single Molecule Imaging of Enhanced Enzyme DiffusionNov 20 2018Recent experimental results have shown that active enzymes can diffuse faster when they are in the presence of their substrates. Fluorescence correlation spectroscopy (FCS), which relies on analyzing the fluctuations in fluorescence intensity signal to ... More
Topological Sieving of Rings According to their RigidityNov 19 2018We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between the rings and ... More
Distance-based Protein Folding Powered by Deep LearningNov 08 2018Nov 12 2018Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed to predict ... More
Binding of Pheophorbide-a methyl ester to nucleic acids of different secondary structures: A spectroscopic studyNov 05 2018Binding of neutral Pheophorbide-a methyl ester (MePheo-a) to various synthetic polynucleotides, double-stranded poly(A)-poly(U), poly(G)-poly(C) and four-stranded poly(G), as well as to calf thymus DNA, was studied using the methods of absorption and ... More
Genomic 3D-compartments emerge from unfolding mitotic chromosomesNov 05 2018The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications, ... More
Deep Robust Framework for Protein Function Prediction using Variable-Length Protein SequencesNov 04 2018Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the functions of the ... More
Generalization of the Elastic Network model for the study of large conformational changes in biomoleculesNov 03 2018The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching of proteins, ... More
Self-assembly of model proteins into virus capsidsNov 02 2018We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described by the structure-based ... More
Single-molecule imaging of DNA gyrase activity in living Escherichia coliNov 01 2018Nov 02 2018Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. Removal of these positive supercoils is essential for replication fork progression and ... More
Temperature-dependent non-covalent protein-protein interactions explain normal and inverted solubility in a mutant of human gamma D-crystallinNov 01 2018Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) ... More
Void distributions reveal structural link between jammed packings and protein coresOct 31 2018Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino acid-shaped ... More
Poly-Sarcosine and Poly(ethylene-glycol) interactions with proteins investigated using molecular dynamics simulationsOct 29 2018Nanoparticles coated with hydrophilic polymers often show a reduction in unspecific interactions with the biological environment, which improves their biocompatibility. The molecular determinants of this reduction are not very well understood yet, and ... More
Relative energetics of acetyl-histidine protomers with and without Zn2+ and a benchmark of energy methodsOct 24 2018We studied acetylhistidine (AcH), bare or microsolvated with a zinc cation by simulations in isolation. First, a global search for minima of the potential energy surface combining both, empirical and first-principles methods, is performed individually ... More
Lattice models and Monte Carlo methods for simulating DNA origami self-assemblyOct 22 2018The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that strikes a balance ... More
Recent advances on the non-coherent band surgery model for site-specific recombinationOct 20 2018Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or ... More
Simulations meet Machine Learning in Structural BiologyOct 19 2018Classical molecular dynamics (MD) simulations will be able to reach sampling in the second timescale within five years, producing petabytes of simulation data at current force field accuracy. Notwithstanding this, MD will still be in the regime of low-throughput, ... More
Advancing Standards-Free Methods for the Identification of Small Molecules in Complex SamplesOct 17 2018The current gold standard for unambiguous identification in metabolomics analysis is based on comparing two or more orthogonal properties from the analysis of authentic, pure reference materials (standards) to experimental data acquired in the same laboratory ... More
Strong deformations of DNA: Effect on the persistence lengthOct 16 2018Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of ... More
Important factors for cell-membrane permeabilization by gold nanoparticles activated by nanosecond-laser irradiationOct 07 2018Purpose: Pulsed-laser irradiation of light-absorbing gold nanoparticles (AuNPs) attached to cells transiently increases cell membrane permeability for targeted molecule delivery. Here, we targeted EGFR on the ovarian carcinoma cell line OVCAR-3 with AuNPs. ... More
Dependence of DNA persistence length on ionic strength and ion typeOct 03 2018Even though the persistence length $L_P$ of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength $I$ lacks a consensual description. Using a high-throughput single-molecule technique and statistical ... More
Lattice nano-ripples revealed in peptide microcrystals by scanning electron nanodiffractionOct 03 2018Changes in lattice structure across sub-regions of protein crystals are challenging to assess when relying on whole crystal measurements. Because of this difficulty, macromolecular structure determination from protein micro and nano crystals requires ... More
Short DNA persistence length in a mesoscopic helical modelSep 29 2018The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available to base pair ... More
Protein token: a dynamic unit in protein interactionsSep 27 2018In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial arrangement of residues, ... More
A natural upper bound to the accuracy of predicting protein stability changes upon mutationsSep 27 2018Accurate prediction of protein stability changes upon single-site variations (DDG) is important for protein design, as well as our understanding of the mechanism of genetic diseases. The performance of high-throughput computational methods to this end ... More
Kinky DNA in solution: Small angle scattering study of a nucleosome positioning sequenceSep 25 2018DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not ... More
RAFP-Pred: Robust Prediction of Antifreeze Proteins using Localized Analysis of n-Peptide CompositionsSep 25 2018In extreme cold weather, living organisms produce Antifreeze Proteins (AFPs) to counter the otherwise lethal intracellular formation of ice. Structures and sequences of various AFPs exhibit a high degree of heterogeneity, consequently the prediction of ... More
Coarse-grained modelling of the structural properties of DNA origamiSep 22 2018We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix bending in ... More
ISiCLE: A molecular collision cross section calculation pipeline for establishing large in silico reference libraries for compound identificationSep 22 2018Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent advances, metabolomics studies ... More
Segregative phase separation scenario of the formation of the bacterial nucleoidSep 19 2018The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, ... More
Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyondSep 19 2018The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from the groove asymmetry ... More
Delineating elastic properties of kinesin linker and their sensitivity to point mutationsSep 18 2018We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. The sample trajectories ... More
Modular decomposition of protein structure using community detectionSep 18 2018As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Protein structures are known to be formed of domains; structural and functional subunits that are often repeated across sets of proteins. ... More
Ligand dissociation mechanisms from all-atom simulations: Are we there yet?Sep 12 2018Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress, together with ... More