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Fibrin formation and mechanical stability are essential in thrombosis and hemostasis. To reveal how mechanical load impacts fibrin, we carried out optical trap-based single-molecule forced unbinding experiments. The strength of noncovalent A:a knob-hole bond stabilizing fibrin polymers first increases with tensile force (catch bonds) and then decreases with force when the force exceeds a critical value (slip bonds). To provide the structural basis of catch–slip-bond behavior, we analyzed crystal structures and performed molecular modeling of A:a knob-hole complex. The movable flap (residues [Formula: see text] 295 to [Formula: see text] 305) containing the weak calcium-binding site [Formula: see text] 2 serves as a tension sensor. Flap dissociation from the B domain in the [Formula: see text]-nodule and translocation to knob ‘A’ triggers hole ‘a’ closure, resulting in the increase of binding affinity and prolonged bond lifetimes. The discovery of biphasic kinetics of knob-hole bond rupture is quantitatively explained by using a theory, formulated in terms of structural transitions in the binding pocket between the low-affinity (slip) and high-affinity (catch) states. We provide a general framework to understand the mechanical response of protein pairs capable of tension-induced remodeling of their association interface. Strengthening of the A:a knob-hole bonds at 30- to 40-pN forces might favor formation of nascent fibrin clots subject to hydrodynamic shear in vivo.

Background A natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A). Methods In this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC. Results Studies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site. Conclusion The NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT. General significance Insights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.

Results of damage and failure investigation in a concrete reinforced by short polymeric fibers are reported in the present work. Two types of fibers were used in experiments 30 mm and 6 mm long. Pull-out experiments were realized, for fibers oriented under different angles to pulling out force direction. Detailed experimental data analysis was performed. Prisms with different concentrations of fibers were fabricated and tested for four point bending. Two numerical models were used for fiber concrete prisms mechanical behavior modeling under four point bending. Modeling results were compared with experimental data.

The number of published materials science articles has increased manyfold over the past few decades. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw text of published articles onto structured database entries that allow for programmatic querying. To this end, we apply text mining with named entity recognition (NER) for large-scale information extraction from the published materials science literature. The NER model is trained to extract summary-level information from materials science documents, including inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifier achieves an accuracy (f1) of 87%, and is applied to information extraction from 3.27 million materials science abstracts. We extract more than 80 million materials-science-related named entities, and the content of each abstract is represented as a database entry in a structured format. We demonstrate that simple database queries can be used to answer complex "meta-questions" of the published literature that would have previously required laborious, manual literature searches to answer. All of our data and functionality has been made freely available on our Github( https://github.com/materialsintelligence/matscholar )and website ( http://matscholar.com ), and we expect these results to accelerate the pace of future materials science discovery.

Over the past decades, the number of published materials science articles has increased manyfold. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw-text of published articles onto a structured database entry that allows for programmatic querying. To this end, we apply text-mining with named entity recognition (NER), along with entity normalization, for large-scale information extraction from the published materials science literature. The NER is based on supervised machine learning with a recurrent neural network architecture, and the model is trained to extract summary-level information from materials science documents, including: inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifer, with an overall accuracy (f1) of 87% on a test set, is applied to information extraction from 3.27 million materials science abstracts - the most information-dense section of published articles.Overall, we extract more than 80 million materials-science-related named entities, and the content of each abstract is represented as a database entry in a structured format. Our database shows far greater recall in document retrieval when compared to traditional text-based searches due to an entity normalization procedure that recognizes synonyms. We demonstrate that simple database queries can be used to answer complex \meta-questions" of the published literature that would have previously required laborious, manual literature searches to answer. All of our data has been made freely available for bulk download; we have also made a public facing application programming interface (https://github.com/materialsintelligence/matscholar) and website http://matscholar.herokuapp.com/search for easy interfacing with the data, trained models and functionality described in this paper. These results will allow researchers to access targeted information on a scale and with a speed that has not been previously available, and can be expected to accelerate the pace of future materials science discovery.

Materials discovery has become significantly facilitated and accelerated by high-throughput ab-initio computations. This ability to rapidly design interesting novel compounds has displaced the materials innovation bottleneck to the development of synthesis routes for the desired material. As there is no a fundamental theory for materials synthesis, one might attempt a data-driven approach for predicting inorganic materials synthesis, but this is impeded by the lack of a comprehensive database containing synthesis processes. To overcome this limitation, we have generated a dataset of “codified recipes” for solid-state synthesis automatically extracted from scientific publications. The dataset consists of 19,488 synthesis entries retrieved from 53,538 solid-state synthesis paragraphs by using text mining and natural language processing approaches. Every entry contains information about target material, starting compounds, operations used and their conditions, as well as the balanced chemical equation of the synthesis reaction. The dataset is publicly available and can be used for data mining of various aspects of inorganic materials synthesis., Measurement(s)solid-state synthesis dataTechnology Type(s)natural language processing Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9906608

Short composite fibres are a relatively new product for concrete disperse reinforcement. In this experimental research, 14 different composite fibres were developed and single fibre pull-out micromechanics was investigated. Three main groups of composite fibre were—composite glass fibres (GF), composite carbon fibres (CF) and hybrid fibres (HF). Composite fibre manufacturing consisted of glass, carbon or combined fibre filament preparation, impregnation with epoxy resin, epoxy curing, quality control and cutting in short discrete macro- fibres. All three composite fibre groups were manufactured with straight, uneven and undulated geometries. Fibre surface finish was smooth and rough. Uneven fibre geometry was achieved by not aligning all fibre filaments in fibre tow. Undulated geometry was a result of interlaced fibres. The rough fibre outer surface finish was achieved by adding an extra layer of epoxy resin containing fine quartz grains. All macro-fibres were cut in 50 mm length. Single fibre pull-out samples with a pre-defined crack between two concrete parts were prepared to investigate fibre pull-out behaviour. Fibre pull-out laws were obtained and analysed. Composite fibre improvement geometry and surface with roughening outer surface made a huge impact on fibre pull-out resistance.

Given the emergence of data science and machine learning throughout all aspects of society, but particularly in the scientific domain, there is increased importance placed on obtaining data. Data in materials science are particularly heterogeneous, based on the significant range in materials classes that are explored and the variety of materials properties that are of interest. This leads to data that range many orders of magnitude, and these data may manifest as numerical text or image-based information, which requires quantitative interpretation. The ability to automatically consume and codify the scientific literature across domains—enabled by techniques adapted from the field of natural language processing—therefore has immense potential to unlock and generate the rich datasets necessary for data science and machine learning. This review focuses on the progress and practices of natural language processing and text mining of materials science literature and highlights opportunities for extracting additional information beyond text contained in figures and tables in articles. We discuss and provide examples for several reasons for the pursuit of natural language processing for materials, including data compilation, hypothesis development, and understanding the trends within and across fields. Current and emerging natural language processing methods along with their applications to materials science are detailed. We, then, discuss natural language processing and data challenges within the materials science domain where future directions may prove valuable.

The overwhelming majority of scientific knowledge is published as text, which is difficult to analyse by either traditional statistical analysis or modern machine learning methods. By contrast, the main source of machine-interpretable data for the materials research community has come from structured property databases1,2, which encompass only a small fraction of the knowledge present in the research literature. Beyond property values, publications contain valuable knowledge regarding the connections and relationships between data items as interpreted by the authors. To improve the identification and use of this knowledge, several studies have focused on the retrieval of information from scientific literature using supervised natural language processing3-10, which requires large hand-labelled datasets for training. Here we show that materials science knowledge present in the published literature can be efficiently encoded as information-dense word embeddings11-13 (vector representations of words) without human labelling or supervision. Without any explicit insertion of chemical knowledge, these embeddings capture complex materials science concepts such as the underlying structure of the periodic table and structure-property relationships in materials. Furthermore, we demonstrate that an unsupervised method can recommend materials for functional applications several years before their discovery. This suggests that latent knowledge regarding future discoveries is to a large extent embedded in past publications. Our findings highlight the possibility of extracting knowledge and relationships from the massive body of scientific literature in a collective manner, and point towards a generalized approach to the mining of scientific literature.

The paper substantiates the possibility of the Russian Post’s participation in the Smart City projects due to the integration of a smart city’s information systems and the postal services’ assets for the collection of the urban data and support of the information processes inherent in the city economy in the information society stage. Integration will improve the results of a smart city’s management and the provision of municipal services to citizens through the use of the technologies underlying the digital economy by the postal services. The transition of the postal authorities from the different countries and the Russian Post to the provision of digital services determines their willingness to become full participants in the Smart City projects launched around the world. The authors present the results of an analysis of international sources and an online survey of the Russian citizens in order to justify the relevance of the research, identify the opinions of the citizens to the Smart City projects, the participation of the Russian Post in the similar projects. The survey reveals the respondents’ attitude to the use of the digital technologies, IoT in the city initiatives, assessment of the potential of the Russian Post in implementing the Smart City projects.

The science in the digital age focuses on interdisciplinary research as the main driver of the development. Modern studies of semantic and thematic contexts taken from the digital scientific resources are important for tasks of information technology use in science, education, management and business. As a rule, interdisciplinary research emerges in response to the trends in social and economic development. Socio-political and cultural environment has also a great influence on the introduction of new terminology into the scientific discourse. The delay of scientific discourse regarding the public discourse generates problems of both scientific and philosophical nature. Furthermore, those challenges influence the education system, making demands for new curricula and courses, which, among other things, reflect the categorical and conceptual basis of the new subject areas. The actual objective is to reveal the trends in the terminological landscape of developing interdisciplinary research directions. The present study offers the Synthetic Method, which combines various approaches and tools of Digital Humanities. This Method allows using context query for the search for information resources; the context knowledge explication and clarification of the terminological landscape of interdisciplinary scientific direction “Digital Economy: e-governance and smart technology”.

Traditional fiberconcrete structures have fibres in the mix oriented in all spatial directions, distributed in the struc­tural element volume homogenously, what not easy to obtain in practice. In many situations, structurally more effective is the insertion of fibres into the concrete structural element body by forming layers, with a predetermined fibre concentration and orientation in every layer. In the present investigation, layered fibre concrete is under investigation. Short steel fibres were at­tached to flexible warps with the necessary fibres concentration and orientation. Warps were placed into the prismatic mould separating them by concrete layers without fibres. Prisms were matured and tested under four-point bending. The bending-affected mechanical behaviour of cracked fibre concrete was simulated numerically by using a developed struc­tural model. Comparing the simulation results with experimental data, material micromechanical fracture mechanisms were analysed and evaluated.

Binding of soluble fibrinogen to the activated conformation of the integrin αIIbβ3 is required for platelet aggregation and is mediated exclusively by the C-terminal AGDV-containing dodecapeptide (γC-12) sequence of the fibrinogen γ chain. However, peptides containing the Arg-Gly-Asp (RGD) sequences located in two places in the fibrinogen Aα chain inhibit soluble fibrinogen binding to αIIbβ3 and make substantial contributions to αIIbβ3 binding when fibrinogen is immobilized and when it is converted to fibrin. Here, we employed optical trap-based nanomechanical measurements and computational molecular modeling to determine the kinetics, energetics, and structural details of cyclic RGDFK (cRGDFK) and γC-12 binding to αIIbβ3. Docking analysis revealed that NMR-determined solution structures of cRGDFK and γC-12 bind to both the open and closed αIIbβ3 conformers at the interface between the αIIb β-propeller domain and the β3 βI domain. The nanomechanical measurements revealed that cRGDFK binds to αIIbβ3 at least as tightly as γC-12. A subsequent analysis of molecular force profiles and the number of peptide-αIIbβ3 binding contacts revealed that both peptides form stable bimolecular complexes with αIIbβ3 that dissociate in the 60-120 pN range. The Gibbs free energy profiles of the αIIbβ3-peptide complexes revealed that the overall stability of the αIIbβ3-cRGDFK complex was comparable with that of the αIIbβ3-γC-12 complex. Thus, these results provide a mechanistic explanation for previous observations that RGD- and AGDV-containing peptides are both potent inhibitors of the αIIbβ3-fibrinogen interactions and are consistent with the observation that RGD motifs, in addition to AGDV, support interaction of αIIbβ3 with immobilized fibrinogen and fibrin.

The present investigation is devoted to simultaneous sorption recovery of copper (II) and zinc (II) ions on some commercial anion exchangers with different physical-chemical properties. The initial concentrations of zinc and copper were 1-3 mmol L-1 and the recovery was carried out in 0.01 M and 2 M hydrochloric acid solutions. It was shown that the investigated anion exchangers possess good sorption and kinetic properties. After the recovery of copper and zinc from strong acidic solutions, their selective elution was carried out by means of 2 M hydrochloric acid solution (zinc recovery) and 2 M ammonia solution (copper recovery). In weak acidic solutions, copper and zinc were separated during sorption, as zinc sorption did not proceed in this case. The subsequent copper (II) elution was carried out by 2 M ammonia solution. The anion exchangers Purolite S985, Purolite A500 and AM-2B can be recommended for zinc and copper recovery from acidic industrial solutions and waste water.

Author(s): Shi, T; Tu, Q; Tian, Y; Xiao, Y; Miara, LJ; Kononova, O; Ceder, G | Abstract: Low active material loading in the composite electrode of all-solid-state batteries (SSBs) is one of the main reasons for the low energy density in current SSBs. In this work, it is demonstrated with both modeling and experiments that in the regime of high cathode loading, the utilization of cathode material in the solid-state composite is highly dependent on the particle size ratio of the cathode to the solid-state conductor. The modeling, confirmed by experimental data, shows that higher cathode loading and therefore an increased energy density can be achieved by increasing the ratio of the cathode to conductor particle size. These results are consistent with ionic percolation being the limiting factor in cold-pressed solid-state cathode materials and provide specific guidelines on how to improve the energy density of composite cathodes for solid-state batteries. By reducing solid electrolyte particle size and increasing the cathode active material particle size, over 50 vol% cathode active material loading with high cathode utilization is able to be experimentally achieved, demonstrating that a commercially-relevant, energy-dense cathode composite is achievable through simple mixing and pressing method.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

X-ray micro-computer tomography (micro-CT) provides 3D visualization of internal geometry of a textile without destructing samples. The objective of this paper is to demonstrate usage of the micro-CT technique for structural analysis of weft-knitted fabrics and to propose a data processing technique for reconstruction and visualization of the loop geometry. The method is applied to glass and steel knitted fabrics. It produces a full description of the loop geometry, namely yarn middle line, cross-section areas and orientation along the yarn.

The transition from -helices to -strands under external mechanical force in fibrin molecule containing coiled-coils is studied and free energy landscape is resolved. The detailed theoretical modeling of each stage of coiled-coils fragment pulling process was performed. The plots of force (F) as a function of molecule expansion (X) for two symmetrical fibrin coiled-coils (each 17 nm in length) show three distinct modes of mechanical behaviour: (1) linear (elastic) mode when coiled-coils behave like entropic springs (F100-125 pN and X7-8 nm), (2) viscous (plastic) mode when molecule resistance force does not increase with increase in elongation length (F150 pN and X10-35 nm) and (3) nonlinear mode (F175-200 pN and X40-50 nm). In linear mode the coiled-coils unwind at 2 radian angle, but no structural transition occurs. Viscous mode is characterized by the phase transition from the triple -spirals to three-stranded parallel -sheet. The critical tension of -helices is 0.25 nm per turn, and the characteristic energy change is equal to 4.9 kcal/mol. Changes in internal energy u, entropy s and force capacity cf per one helical turn for phase transition were also computed. The observed dynamic behavior of -helices and phase transition from -helices to -sheets under tension might represent a universal mechanism of regulation of fibrillar protein structures subject to mechanical stresses due to biological forces.

The present work studies the possibility to decrease the formation of micro and nano cracks around short fibres in fibre-reinforced concrete (FRC) composite with the help of nano-reinforcement, which is carbon nanotubes, or micro reinforcement, which is carbon short fibres and nano-fillers. Tensile and bending strength of FRC depends on the spatial distribution of fibres inside a material, type of fibre and cement matrix, as well as an effective micromechanical work of each fibre while pulling out of the concrete matrix. Shrinkage stresses, acting in the matrix in the vicinity of a fibre, lead to the formation of micro-cracks. Such micro-cracks were observed experimentally and were investigated numerically performing broad modelling based on the finite element method (FEM). The investigation was focused on the micromechanical behaviour of a single steel fibre in a cement matrix. Numerical modelling results demonstrated a high level of shrinkage overstresses around steel fibres in concrete. The role of nano and micro admixtures, nanotubes, short carbon fibres as well as the role of water/cement ratio in a high performance concrete matrix, changing (increasing or decreasing) the friction force between the matrix and the steel fibre, were investigated experimentally by way of per­forming a single fibre pull-out tests. The high scatters of experimental results were obtained in performed pull-out tests. At the same time, for the same series of samples, a positive role of micro and nano admixtures and carbon nanotubes in the increase of pull-out force was recognised.

Hydrodynamic interactions (HI) are incorporated into Langevin dynamics of the Cα‐based protein model using the Truncated Expansion approximation (TEA) to the Rotne–Prager–Yamakawa diffusion tensor. Computational performance of the obtained GPU realization demonstrates the model's capability for describing protein systems of varying complexity (102–105 residues), including biological particles (filaments, virus shells). Comparison of numerical accuracy of the TEA versus exact description of HI reveals similar results for the kinetics and thermodynamics of protein unfolding. The HI speed up and couple biomolecular transitions through cross‐communication among protein domains, which result in more collective displacements of structure elements governed by more deterministic (less variable) dynamics. The force‐extension/deformation spectra from nanomanipulations in silico exhibit sharper force signals that match well the experimental profiles. Hence, biomolecular simulations without HI overestimate the role of tension/stress fluctuations. Our findings establish the importance of incorporating implicit water‐mediated many‐body effects into theoretical modeling of dynamic processes involving biomolecules. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

The article discusses an approach of coordinating university scientific activities with using contextual search and contextual knowledge extraction technologies. For the implementation of the proposed approach, the authors use an e-library «Humanitariana» with services of contextual search, different types of queries, automated extraction of knowledge from the scientific texts. The advantage of using «Humanitariana» is in the possibility of combining the resources of several organizations, which can function in a local network mode and in distributed IT environment with ability to appeal to all resources from any of the servers of participating organizations. The approach was created and tested in context of preparation of master’s theses in “Applied Computer Science” (ITMO University) and scientific exploratory research (The Sociological Institute of the RAS).

Computer games are the new research theme for social scientists and humanitarians with increased interest over the past 10–15 years. To evaluate the dynamics of research interest to the different thematic aspects of computer games expansion we made the review of the Russian scientific journals for the period 2005–2016 by the e-Library «Humanitariana» having the function of a flexible thematic full-text search. This information system is developed at the ITMO University. We used the methods of frequency-oriented search. We analyzed material of articles (N = 601) which were placed on the portal e-LIBRARY (http://elibrary.ru/).

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}\end{document}Cα-based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.

The research paper addresses the issue of the impact of MMORPGs on social culture and communication skills of individuals. The mainstream discourse about computer games which take individuals away from reality and substitute the real life by the fictional one is complemented by brand new ideas, which affirm that computer games do not substitute but supplement the real life and expand its possibilities. To confirm the presented point of view we use diagnostic questionnaire of interpersonal relations by A.A. Rukavishnikov. This questionnaire is aimed to evaluate typical ways of respondent’s attitude towards other people. At this point we have 43 gamers and 29 non-gamers involved in our research, aged 18 to 57. The comparison of a user and non-user answers gives a bigger view on an overall gaming experience. In the obtained indices we note that there are no fundamental differences between MMORPGs gamers and ordinary people. During research, MMORPGs users have showed many important social interaction skills such as striving to control own actions, collaborate with others, though with a low interest in emotionally charged relationships. Authors discuss the idea about the differences between addiction and fascination among gamers.

Interest to structural application of textile reinforced polymer matrix composite materials (CM) is growing during last years. In different branches of machine building, aerospace, automotive and others industries we can find structural elements preferably be produced using such reinforcement. At the same time, such materials are exhibiting elastic and strength properties scatter. In the framework of the present investigation, we observe yarn penetrated by a resin in a composite as a reinforcing “macro” fiber. Such “macro” fiber mechanical properties were measured experimentally, for this purpose was produced and was tested by tension until fracture fiber samples, having different length. Then was elaborated and was realized structural strength probabilistic model. In the textile geometry, was picked out repeating structural element – polymer matrix volume with two curved “macro” fiber’s chunks inside it. Complete composite material volume is possible to represent as a set of repeating structural elements. External loads application leads to disperse structural elements failure. Neighboring to ruptured elements are overloaded leading to higher probability to fail for them. Using FEM was modeled stress state in “macro” fibers inside CM. Then, was numerically obtained stress distribution in composite material, having different number of broken loops. Probabilities of different numbers of failed elements were calculated. Strength probability function, based on Weibull approach was obtained. CM samples were tested under tension and obtained results were compared with numerical modeling as well as were analyzed.

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physico-chemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force-deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the reversible dissociation of lateral bonds followed by irreversible dissociation of the longitudinal bonds. We have determined the free energies of dissociation of the lateral (6.9+/-0.4 kcal/mol) and longitudinal (14.9+/-1.5 kcal/mol) tubulin-tubulin bonds. These values in conjunction with the large flexural rigidity of tubulin protofilaments obtained (18,000-26,000 pN*nm^2), support the idea that the disassembling microtubule is capable of generating a large mechanical force to move chromosomes during cell division. Our computational modeling offers a comprehensive quantitative platform to link molecular tubulin characteristics with the physiological behavior of microtubules. The developed in silico nanoindentation method provides a powerful tool for the exploration of biomechanical properties of other cytoskeletal and multiprotein assemblies

Physical properties of capsids of plant and animal viruses are important factors in capsid self-assembly, survival of viruses in the extracellular environment, and their cell infectivity. Combined AFM experiments and computational modeling on subsecond timescales of the indentation nanomechanics of Cowpea Chlorotic Mottle Virus capsid show that the capsid's physical properties are dynamic and local characteristics of the structure, which change with the depth of indentation and depend on the magnitude and geometry of mechanical input. Under large deformations, the Cowpea Chlorotic Mottle Virus capsid transitions to the collapsed state without substantial local structural alterations. The enthalpy change in this deformation state Delta H-ind =11.5-12.8 MJ/mol is mostly due to large-amplitude out-of-plane excitations, which contribute to the capsid bending; the entropy change T Delta S-ind = 5.1-5.8 MJ/mol is due to coherent in-plane rearrangements of protein chains, which mediate the capsid stiffening. Direct coupling of these modes defines the extent of (ir)reversibility of capsid indentation dynamics correlated with its (in)elastic mechanical response to the compressive force. This emerging picture illuminates how unique physico-chemical properties of protein nanoshells help define their structure and morphology, and determine their viruses' biological function.

Botulinum neurotoxin (BoNT), the most toxic substance known to mankind, is the first example of the fully active molten globule state. To understand its folding mechanism, we performed urea denaturation experiments and theoretical modeling using BoNT serotype A (BoNT/A). We found that the extent of BoNT/A denaturation from the native state (N) shows a nonmonotonic dependence on urea concentration indicating a unique multistep denaturation process, N → I1I2U, with two intermediate states I1 and I2. BoNT/A loses almost all its secondary structure in 3.75 M urea (I1), yet it displays a native-like secondary structure in 5 M urea (I2). This agrees with the results of theoretical modeling, which helped to determine the molecular basis of unique behavior of BoNT/A in solution. Except for I2, all the states revert back to full enzymatic activity for SNAP-25 including the unfolded state U stable in 7 M urea. Our results stress the importance of structural flexibility in the toxin’s mechanism of survival and action, an unmatched evolutionary trait from billion-year-old bacteria, which also correlates with the long-lasting enzymatic activity of BoNT inside neuronal cells. BoNT/A provides a rich model to explore protein folding in relation to functional activity.

Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force–deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the transition regime, during which the microtubule lattice undergoes discrete structural changes, which include first the revers...

Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs ‘A’ and ‘B’ in the central nodule of fibrin monomer to complementary holes ‘a’ and ‘b’ in the γ- and β-nodules, respectively, of another monomer. We characterized the A:a and B:b knob-hole interactions under varying solution conditions using molecular dynamics simulations of the structural models of fibrin(ogen) fragment D complexed with synthetic peptides GPRP (knob ‘A’ mimetic) and GHRP (knob ‘B’ mimetic). The strength of A:a and B:b knob-hole complexes was roughly equal, decreasing with pulling force; however, the dissociation kinetics were sensitive to variations in acidity (pH 5–7) and temperature (T = 25–37 °C). There were similar structural changes in holes ‘a’ and ‘b’ during forced dissociation of the knob-hole complexes: elongation of loop I, stretching of the interior region, and translocation of the moveable flap. The disruption of the knob-hole interactions was not an “all-or-none” transition as it occurred through distinct two-step or single step pathways with or without intermediate states. The knob-hole bonds were stronger, tighter, and more brittle at pH 7 than at pH 5. The B:b knob-hole bonds were weaker, looser, and more compliant than the A:a knob-hole bonds at pH 7 but stronger, tighter, and less compliant at pH 5. Surprisingly, the knob-hole bonds were stronger, not weaker, at elevated temperature (T = 37 °C) compared with T = 25 °C due to the helix-to-coil transition in loop I that helps stabilize the bonds. These results provide detailed qualitative and quantitative characteristics underlying the most significant non-covalent interactions involved in fibrin polymerization.

Binding of soluble fibrinogen to the activated open conformation of the integrin αIIbβ3 is required for platelet aggregation and is mediated exclusively by the C-terminal AGDV-containing dodecapeptide (γC-12) sequence of the fibrinogen γ chain. Paradoxically, however, peptides containing the Arg-Gly-Asp (RGD) sequences located in two places in the fibrinogen Aα chain inhibit soluble fibrinogen binding to αIIbβ3. Moreover, the Aα chain RGD motifs make substantial contributions to αIIbβ3 binding when fibrinogen is immobilized and when it is converted to fibrin. The interaction of αIIbβ3 with a variety of RGD- and γC-12 peptides has been studied extensively, but the characteristics of their binding to the active open and inactive closed conformations of αIIbβ3 are largely unknown. Here, we have used both experimental and computational approaches to compare the two-dimensional kinetics, thermodynamics and structural details of cyclic RGDFK (cRGDFK) and γC-12 binding to αIIbβ3. First, we employed optical trap-based single-molecule nanomechanical measurements to determine the probability of peptide binding to αIIbβ3 as a function of the time the peptides interact with αIIbβ3. In the optical trap-based experimental system, a microscopic bead coated with either cRGDFK or γC-12 is trapped in a fluid chamber by a focused laser beam and moved in an oscillatory manner to touch a stationary pedestal coated with αIIbβ3. When the peptide on the bead interacts with αIIbβ3 on the pedestal, tension is generated when the bead is displaced from the laser focus until the αIIbβ3-peptide bond ruptures. The percentage of binding/unbinding events at a particular time of contact duration enabled us to plot the force-free binding probability as a function of contact duration. From these curves, we extracted first-order binding rates: 0.61×10-14 cm2/s for γC-12 and 0.71×10-14 cm2/s for cRGDFK and unbinding rates: 2.05/s and 1.53/s for the γC-12 and cRGDFK, respectively. Corresponding binding affinity constants were 0.3×10-14 cm2 and 0.46×10-14 cm2 for the γC-12 and cRGDFK, respectively, indicating that cRGDFK binds to αIIbβ3 somewhat tighter than γC-12. These measurements were then followed by computational modeling using NMR-determined 3D solution structures of cRGDFK and γC-12, as well as the crystallographically resolved αIIbβ3 conformers of the αIIbβ3 headpiece (PDB entries: 3ZDX and 3ZE2). Docking analysis confirmed that both cRGDFK and γC-12 bound to the αIIbβ3 conformers at a site located in the interface between the α subunit β-propeller domain and the β subunit βI domain. Estimated docking energies revealed that the closed αIIbβ3 conformation is almost as reactive towards the peptides as the open conformation. Next, we probed the strength of the αIIbβ3-peptide interactions and determined their comparative binding energies and the dynamics of interatomic contacts by performing dynamic force-ramp unbinding in silico using all-atom Molecular Dynamics simulations in implicit solvent on Graphics Processing Units. Force was increased linearly at a pulling rate of 2×104 μm/s and applied to specified Cα-atom of the peptides. Analysis of the molecular force profiles and the number of ligand-receptor binding contacts revealed that both peptides interact strongly with αIIbβ3, forming stable bimolecular complexes that dissociate in the 60-120 pN range through several competing unbinding pathways that display multi-step kinetics and distinct bond lifetimes. We profiled the Gibbs free energy (ΔG) of the αIIbβ3-peptide complexes as a function of the separation distance between the open form of αIIbβ3 headpiece and the peptide using the Umbrella Sampling technique. The results showed that the energies of ligand binding to the αIIbβ3 headpiece are ΔG~16 kcal/mol for cRGDFK and ΔG~13 kcal/mol for γC-12, meaning that the overall thermodynamic stability of the αIIbβ3-peptide complex is higher for cRGDFK than for γC-12. Thus, these results provide a kinetic and thermodynamic explanation for previous observations that the affinity of RGD for αIIbβ3 is greater than AGDV and support our hypothesis that the RGD motifs preferentially support the interaction of αIIbβ3 with immobilized fibrinogen and fibrin. Disclosures Weisel: Bayer: Research Funding.

We characterized the α-to-β transition in α-helical coiled-coil connectors of human fibrin(ogen) molecule using biomolecular simulations of their forced elongation, and theoretical modeling. The force (F) - extension (X) profiles show three distinct regimes: (1) the elastic regime, in which the coiled-coils act as entropic springs (F < 100–125 pN; X < 7–8 nm); (2) the constant-force plastic regime, characterized by a force-plateau (F≈150 pN; X≈10–35 nm); and (3) the non-linear regime (F >175–200 pN; X > 40–50 nm). In the plastic regime, the three-stranded α-helices undergo a non-cooperative phase transition to form parallel three-stranded β-sheets. The critical extension of α-helices is 0.25 nm, and the energy difference between the α-helices and β-sheets is 4.9 kcal/mol per helical pitch. The soft α-to-β phase transition in coiled-coils might be a universal mechanism underlying mechanical properties of filamentous α-helical proteins.

Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of protein-protein interactions. By utilizing the GPU-based computational acceleration, we carried out simulations of the protein forced unfolding for the dimer WW-WW of the all-beta-sheet WW domains used as a model multidomain protein. We found that while the physically non-interacting identical protein domains (WW) show nearly symmetric mechanical properties at low tension, reflected, e.g., in the similarity of their distributions of unfolding times, these properties become distinctly different when tension is increased. Moreover, the uncorrelated unfolding transitions at a low pulling force become increasingly more correlated (dependent) at higher forces. Hence, the applied force not only breaks "the mechanical symmetry" but also couples the physically non-interacting protein domains forming a multi-domain protein. We call this effect "the topological coupling". We developed a new theory, inspired by Order statistics, to characterize protein-protein interactions in multi-domain proteins. The method utilizes the squared-Gaussian model, but it can also be used in conjunction with other parametric models for the distribution of unfolding times. The formalism can be taken to the single-molecule experimental lab to probe mechanical cooperativity and domain communication in multi-domain proteins.

Abstract 2217 A new field of biomedical research, biomechanics of hemostasis and thrombosis, has been quickly developing over the past few years. The mechanical properties of fibrin are essential in vivo for the ability of clots to stop bleeding in flowing blood but also determine the likelihood of obstructive thrombi that cause heart attack and stroke. Despite such critical importance, the structural basis of clot mechanics is not well understood. The structural changes underlying deformation of fibrin polymer occur at different spatial scales from macroscopic to submolecular, including molecular unfolding, about which relatively little is known. In this work, fibrin mechanics was studied with respect to molecular structural changes during fibrin deformation. The results of atomic force microscopy-induced unfolding of fibrinogen monomers and oligomers were correlated with force-extension curves obtained using Molecular Dynamics simulations. The mechanical unraveling of fibrin(ogen) was shown to be determined by molecular transitions that couple reversible extension-contraction of the α-helical coiled-coil regions with unfolding of the terminal γ-nodules. The coiled-coils act as molecular springs to buffer external mechanical perturbations, transmitting and distributing force as the γ-nodules unfold. Unfolding of the γ-nodules, stabilized by strong inter-domain interactions with the neighboring β-nodules, was characterized by an average force of ∼90 pN and peak-to-peak distance of ∼25 nm. All-atom Molecular Dynamics simulations further showed a transition from α-helix to β-sheet at higher extensions. To reveal the force-induced α-helix to β-sheet transition in fibrin experimentally, we used Fourier Transform infrared spectroscopy of hydrated fibrin clots made from human blood plasma. When extended or compressed, fibrin showed a shift of absorbance intensity mainly in the amide I band but also in the amide II and III bands, demonstrating an increase of the β-sheets and a corresponding reduction of the α-helices. These structural conversions correlated directly with the strain or pressure and were partially reversible at the conditions applied. The spectra characteristic of the nascent inter-chain β-sheets were consistent with protein aggregation and fiber bundling during clot deformation observed using scanning electron microscopy. Additional information on the mechanically induced α-helix to β-sheet transition in fibrin was obtained from computational studies of the forced elongation of the entire fibrin molecule and its α-helical coiled-coil portions. We found that upon force application, the coiled-coils undergo ∼5–50 nm extension and 360-degree unwinding. The force-extension curves for the coiled-coils showed three distinct regimes: the linear elastic regime, the constant-force plastic regime, and the non-linear regime. In the linear regime, the coiled-coils unwind but not unfold. In the plastic regime, the triple α-helical segments rewind and re-unwind while undergoing a non-cooperative phase transition to form parallel β-sheets. We conclude that under extension and/or compression an α-helix to β-sheet conversion of the coiled-coils occurs in the fibrin clot as a part of forced protein unfolding. These regimes of forced elongation of fibrin provide important qualitative and quantitative characteristics of the molecular mechanisms underlying fibrin mechanical properties at the microscopic and macroscopic scales. Furthermore, these structural characteristics of the dynamic mechanical behavior of fibrin at the nanometer scale determine whether or not clots have the strength to stanch bleeding and if thrombi become obstructive or embolize. Finally, this knowledge of the functional significance of different domains of fibrin(ogen) suggests new approaches for modulation of these properties as potential therapeutic interventions. Disclosures: No relevant conflicts of interest to declare.