scholarly journals Length of Mucin-Like Domains Enhance Cell-Ebola Virus Adhesion by Increasing Binding Probability

2020 ◽  
Author(s):  
X. Cui ◽  
N. Lapinski ◽  
X. Zhang ◽  
A. Jagota
Keyword(s):  
Ebola Virus ◽  
Molecular Model ◽  
Persistence Length ◽  
Experimental Studies ◽  
Coarse Grained ◽  
Physiological Processes ◽  
Initial Adhesion ◽  
Binding Probability ◽  
A Cell ◽  
Coated Surface

AbstractThe Ebola virus (EBOV) hijacks normal physiological processes by apoptotic mimicry in order to be taken up by the cell it infects. The initial adhesion of the virus to the cell is based on the interaction between T-cell immunoglobulin and mucin domain protein, TIM, on the cell-surface and phosphatidylserine (PS) on the viral outer surface. Therefore, it is important to understand the interaction between EBOV/PS and TIM, with selective blocking of the interaction as a potential therapy. Recent experimental studies have shown that for TIM-dependent EBOV entry, a Mucin-like Domain (MLD) with a length of at least 120 amino acids is required, possibly due to the increase of area of the PS-coated surface sampled. We examine this hypothesis by modeling the process of TIM-PS adhesion using a coarse-grained molecular model. We find that the strength of bound PS−TIM pairs is essentially independent of TIM length. TIMs with longer MLDs have higher average binding strengths because of an increase in the probability of binding between EBOV and TIM proteins. Similarly, we find that for larger persistence length (less flexible) the average binding force decreases, again because of a reduction in the probability of binding.Statement of SignificanceThis work studies the mechanism of TIM-dependent adhesion of the Ebola virus to a cell. Through coarse grained modeling we show that longer TIM stalks adhere more easily as they can sample a larger area, thus offering a mechanistic interpretation of an experimental finding. Better mechanistic understanding can lead to therapeutic ideas for blocking adhesion.

scholarly journals Mechanical Interactions between a Cell and an Extracellular Environment Facilitate Durotactic Cell Migration

2018 ◽  
Author(s):  
Abdel-Rahman Hassan ◽  
Thomas Biel ◽  
Taeyoon Kim
Keyword(s):  
Cell Migration ◽  
Computational Models ◽  
Biomechanical Model ◽  
Coarse Grained ◽  
Physiological Processes ◽  
Specific Direction ◽  
A Cell ◽  
Stiffness Profile ◽  
Contractile Forces ◽  
Extracellular Environment

ABSTRACTCell migration is a fundamental process in biological systems, playing an important role for diverse physiological processes. Cells often exhibit directed migration in a specific direction in response to various types of cues. In particular, cells are able to sense the rigidity of surrounding environments and then migrate towards stiffer regions. To understand this mechanosensitive behavior called durotaxis, several computational models have been developed. However, most of the models made phenomenological assumptions to recapitulate durotactic behaviors, significantly limiting insights provided from these studies. In this study, we developed a computational biomechanical model without any phenomenological assumption to illuminate intrinsic mechanisms of durotactic behaviors of cells migrating on a two-dimensional substrate. The model consists of a simplified cell generating contractile forces and a deformable substrate coarse-grained into an irregular triangulated mesh. Using the model, we demonstrated that durotactic behaviors emerge from purely mechanical interactions between the cell and the underlying substrate. We investigated how durotactic migration is regulated by biophysical properties of the substrate, including elasticity, viscosity, and stiffness profile.

Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes

2019 ◽  
Vol 26 (21) ◽  
pp. 3890-3910 ◽  
Author(s):  
Branislava Gemovic ◽  
Neven Sumonja ◽  
Radoslav Davidovic ◽  
Vladimir Perovic ◽  
Nevena Veljkovic
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Experimental Studies ◽  
Protein Protein Interactions ◽  
Web Based ◽  
Prediction Tools ◽  
Physiological Processes ◽  
Modern Drug ◽  
Ppi Prediction

Background: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this, we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology. Objective: Here, we will review community available computational programs for predicting PPIs and web-based resources for storing experimentally annotated interactions. Methods: We compared the capacities of prediction tools: iLoops, Struck2Net, HOMCOS, COTH, PrePPI, InterPreTS and PRISM to predict recently discovered protein interactions. Results: We described sequence-based and structure-based PPI prediction tools and addressed their peculiarities. Additionally, since the usefulness of prediction algorithms critically depends on the quality and quantity of the experimental data they are built on; we extensively discussed community resources for protein interactions. We focused on the active and recently updated primary and secondary PPI databases, repositories specialized to the subject or species, as well as databases that include both experimental and predicted PPIs. Conclusion: PPI complexes are the basis of important physiological processes and therefore, possible targets for cell-penetrating ligands. Reliable computational PPI predictions can speed up new target discoveries through prioritization of therapeutically relevant protein–protein complexes for experimental studies.

scholarly journals Understanding sex differences in long-term blood pressure regulation: insights from experimental studies and computational modeling

2019 ◽  
Vol 316 (5) ◽  
pp. H1113-H1123 ◽  
Author(s):  
Sameed Ahmed ◽  
Rui Hu ◽  
Jessica Leete ◽  
Anita T. Layton
Keyword(s):  
Blood Pressure ◽  
Sex Differences ◽  
Computational Models ◽  
Experimental Studies ◽  
Pressure Control ◽  
Blood Pressure Regulation ◽  
Pressure Regulation ◽  
Physiological Processes ◽  
Key Players

Sex differences in blood pressure and the prevalence of hypertension are found in humans and animal models. Moreover, there has been a recent explosion of data concerning sex differences in nitric oxide, the renin-angiotensin-aldosterone system, inflammation, and kidney function. These data have the potential to reveal the mechanisms underlying male-female differences in blood pressure control. To elucidate the interactions among the multitude of physiological processes involved, one may apply computational models. In this review, we describe published computational models that represent key players in blood pressure regulation, and highlight sex-specific models and their findings.

Structure and Hardness of Cryorolled and Heat-Treated 2xxx Aluminum Alloy

2010 ◽  
Vol 667-669 ◽  
pp. 925-930
Author(s):  
S.V. Krymskiy ◽  
Elena Avtokratova ◽  
M.V. Markushev ◽  
Maxim Yu. Murashkin ◽  
O.S. Sitdikov
Keyword(s):  
Heat Treatment ◽  
Solid Solution ◽  
Plastic Deformation ◽  
Aluminum Alloy ◽  
Severe Plastic Deformation ◽  
Coarse Grained ◽  
Aging Response ◽  
Heat Treated ◽  
Aluminum Solid Solution ◽  
A Cell

The effects of severe plastic deformation (SPD) by isothermal rolling at the temperature of liquid nitrogen combined with prior- and post-SPD heat treatment, on microstructure and hardness of Al-4.4%Cu-1.4%Mg-0.7%Mn (D16) alloy were investigated. It was found no nanostructuring even after straining to 75%. Сryodeformation leads to microshear banding and processing the high-density dislocation substructures with a cell size of ~ 100-200 nm. Such a structure remains almost stable under 1 hr annealing up to 200oC and with further temperature increase initially transforms to bimodal with a small fraction of nanograins and then to uniform coarse grained one. It is found the change in the alloy post–SPD aging response leading to more active decomposition of the preliminary supersaturated aluminum solid solution, and to the alloy extra hardening under aging with shorter times and at lower temperatures compared to T6 temper.

scholarly journals FOLDING ELASTIC TRANSMEMBRANE HELICES TO FIT IN A LOW-RESOLUTION IMAGE BY ELECTRON MICROSCOPY

2011 ◽  
Vol 09 (supp01) ◽  
pp. 37-50 ◽  
Author(s):  
YUTAKA UENO ◽  
KAZUNORI KAWASAKI ◽  
OSAMU SAITO ◽  
MASAFUMI ARAI ◽  
MAKIKO SUWA
Keyword(s):  
Membrane Proteins ◽  
Structure Prediction ◽  
Molecular Model ◽  
Imaging Techniques ◽  
Transmembrane Helix ◽  
Prediction Method ◽  
Molecular Shape ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Low Resolution

Structure prediction of membrane proteins could be constrained and thereby improved by introducing data of the observed molecular shape. We studied a coarse-grained molecular model that relied on residue-based dummy atoms to fold the transmembrane helices of a protein in the observed molecular shape. Based on the inter-residue potential, the α-helices were folded to contact each other in a simulated annealing protocol to search optimized conformation. Fitting the model into a three-dimensional volume was tested for proteins with known structures and resulted in a fairly reasonable arrangement of helices. In addition, the constraint to the packing transmembrane helix with the two-dimensional region was tested and found to work as a very similar folding guide. The obtained models nicely represented α-helices with the desired slight bend. Our structure prediction method for membrane proteins well demonstrated reasonable folding results using a low-resolution structural constraint introduced from recent cell-surface imaging techniques.

scholarly journals Neuroprotective Function of 14-3-3 Proteins in Neurodegeneration

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Tadayuki Shimada ◽  
Alyson E. Fournier ◽  
Kanato Yamagata
Keyword(s):  
Neurodegenerative Disease ◽  
Cellular Localization ◽  
Experimental Studies ◽  
Adaptor Proteins ◽  
Vast Number ◽  
Physiological Processes ◽  
Binding Partners ◽  
Neuroprotective Function ◽  
And Function ◽  
Regulation Of Enzyme Activity

14-3-3 proteins are abundantly expressed adaptor proteins that interact with a vast number of binding partners to regulate their cellular localization and function. They regulate substrate function in a number of ways including protection from dephosphorylation, regulation of enzyme activity, formation of ternary complexes and sequestration. The diversity of 14-3-3 interacting partners thus enables 14-3-3 proteins to impact a wide variety of cellular and physiological processes. 14-3-3 proteins are broadly expressed in the brain, and clinical and experimental studies have implicated 14-3-3 proteins in neurodegenerative disease. A recurring theme is that 14-3-3 proteins play important roles in pathogenesis through regulating the subcellular localization of target proteins. Here, we review the evidence that 14-3-3 proteins regulate aspects of neurodegenerative disease with a focus on their protective roles against neurodegeneration.

scholarly journals Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

2018 ◽  
Author(s):  
Debayan Chakraborty ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Electrostatic Interactions ◽  
Persistence Length ◽  
Data Bank ◽  
Coarse Grained ◽  
Force Extension ◽  
Sequence Dependence ◽  
Coarse Grained Model ◽  
Interaction Sites ◽  
Double Stranded Dna ◽  
Centers Of Mass

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

scholarly journals Tensins – emerging insights into their domain functions, biological roles and disease relevance

2021 ◽  
Vol 134 (4) ◽  
pp. jcs254029
Author(s):  
Yi-Chun Liao ◽  
Su Hao Lo
Keyword(s):  
Focal Adhesion ◽  
Muscle Regeneration ◽  
Normal Tissue ◽  
Physiological Processes ◽  
Focal Adhesion Proteins ◽  
A Cell ◽  
Disease Relevance ◽  
Cytoskeletal Networks ◽  
Multiple Domains ◽  
Mechanical Sensing

ABSTRACTTensins are a family of focal adhesion proteins consisting of four members in mammals (TNS1, TNS2, TNS3 and TNS4). Their multiple domains and activities contribute to the molecular linkage between the extracellular matrix and cytoskeletal networks, as well as mediating signal transduction pathways, leading to a variety of physiological processes, including cell proliferation, attachment, migration and mechanical sensing in a cell. Tensins are required for maintaining normal tissue structures and functions, especially in the kidney and heart, as well as in muscle regeneration, in animals. This Review discusses our current understanding of the domain functions and biological roles of tensins in cells and mice, as well as highlighting their relevance to human diseases.

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