Search for: protein-conformation
A theoretical study of repeating sequence in HRP II: A combination of molecular dynamics simulations and 17O quadrupole coupling tensors, Article Biophysical Chemistry ; Volume 137, Issue 2-3 , 2008 , Pages 76-80 ; 03014622 (ISSN) ; Esrafili, M. D ; van der spoel, D ; Hadipour, N. L ; Parsafar, G ; Sharif University of Technology
Histidine rich protein II derived peptide (HRP II 169-182) was investigated by molecular dynamics, MD, simulation and 17O electric field gradient, EFG, tensor calculations. MD simulation was performed in water at 300 K with α-helix initial structure. It was found that peptide loses its initial α-helix structure rapidly and is converted to random coil and bent secondary structures. To understand how peptide structure affects EFG tensors, initial structure and final conformations resulting from MD simulations were used to calculate 17O EFG tensors of backbone carbonyl oxygens. Calculations were performed using B3LYP method and 6-31 + G* basis set. Calculated 17O EFG tensors were used to...
Article Journal of Chemical Physics ; Volume 128, Issue 11 , 2008 ; 00219606 (ISSN) ; Rahimi Tabar, M. R ; Sahimi, M ; Sharif University of Technology
Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of α -de novo-designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's...
Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used...
Binding assessment of two arachidonic-based synthetic derivatives of adrenalin with β-lactoglobulin: Molecular modeling and chemometrics approach, Article Biophysical Chemistry ; Volume 207 , 2015 , Pages 97-106 ; 03014622 (ISSN) ; Bordbar, A. K ; Akvan, N ; Parastar, H ; Fani, N ; Gretskaya, N. M ; Bezuglov, V. V ; Haertlé, T ; Sharif University of Technology
A computational approach to predict the main binding modes of two adrenalin derivatives, arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) with the β-lactoglubuline (BLG) as a nano-milk protein carrier is presented and assessed by comparison to the UV-Vis absorption spectroscopic data using chemometric analysis. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm led to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the apparent equilibrium constants computation. The negative values of entropy and enthalpy changes for both compound indicated...
Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 93, Issue 1 , 2016 ; 15393755 (ISSN) ; Khoshnood, A ; Jalali, M. A ; Sharif University of Technology
American Physical Society
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α-helices and β-sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch,...
Article Biomedical Optics Express ; Volume 9, Issue 3 , 2018 ; 21567085 (ISSN) ; Babaei, M ; Azadbakht, A ; Pazoki Toroudi, H ; Mashaghi, A ; Moosavi Movahedi, A. A ; Seyed Reihani, .N ; Sharif University of Technology
OSA - The Optical Society 2018
Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America
Article FEBS Journal ; Volume 286, Issue 6 , 2019 , Pages 1230-1239 ; 1742464X (ISSN) ; Guasch, A ; Biçer, A ; Aranguren Ibáñez, Á ; Chashmniam, S ; Paniagua, J. C ; Pérez Riba, M ; Fita, I ; Pons, M ; Sharif University of Technology
Blackwell Publishing Ltd 2019
Calcineurin is an essential calcium-activated serine/threonine phosphatase. The six NMR-observable methionine methyl groups in the catalytic domain of human calcineurin Aα (CNA) were assigned and used as reporters of the presence of potential cis-trans isomers in solution. Proline 84 is found in the cis conformation in most calcineurin X-ray structures, and proline 309, which is part of a highly conserved motif in phosphoprotein phosphatases, was modeled with a cis peptide bond in one of the two molecules present in the asymmetric unit of CNA. We mutated each of the two prolines to alanine to force the trans conformation. Solution NMR shows that the P84A CNA mutant exists in two forms,...
α-Helical antimicrobial peptide encapsulation and release from boron nitride nanotubes: A computational study, Article International Journal of Nanomedicine ; Pages 4277-4288 , Volume 16 , 2021 ; 11769114 (ISSN) ; Yousefi, F ; Bagheri, B ; Seidi, F ; Mashhadzadeh, A. H ; Rabiee, N ; Zarrintaj, P ; Mostafavi, E ; Saeb, M. R ; Kim, Y. C ; Sharif University of Technology
Dove Medical Press Ltd 2021
Introduction: Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage. Methods: Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation. Results: The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to −270 kcal·mol−1 at the end of the simulation (15 ns). However, during the period of 0.2–1.8 ns, when half of the peptide was inside the nanotube, the...
Article International Journal of Nanomedicine ; Volume 16 , 2021 , Pages 1837-1847 ; 11769114 (ISSN) ; Bagheri, B ; Yousefi, F ; Nasiriasayesh, A ; Mashhadzadeh, A. H ; Zarrintaj, P ; Rabiee, N ; Bagherzadeh, M ; Fierro, V ; Celzard, A ; Saeb, M. R ; Mostafavi, E ; Sharif University of Technology
Dove Medical Press Ltd 2021
Introduction: Nanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance. Methods: In this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation. Results: The peptide was absorbed into the BNNT by van der Waals (vdW)...
Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 72, Issue 6 , 2005 ; 15393755 (ISSN) ; Farzami, R. R ; Ejtehadi, M. R ; Sharif University of Technology
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of...
Article Current Opinion in Colloid and Interface Science ; Vol. 19, issue. 6 , 2014 , pp. 514-519 ; ISSN: 13590294 ; Lotfi, M ; Kragel, J ; Javadi, A ; Bastani, D ; Miller, R ; Sharif University of Technology
Dilational and shear viscoelasticities are important properties of interfacial layers. These quantities are particularly relevant in all systems which contain a huge internal interfacial area such as foams and emulsions. Therefore, also the 3D rheological behavior of foams or emulsions studied by respective methods is superimposed by the 2D interfacial rheology.We report on recent developments in dilational and shear rheology from an experimental point of view as well as discuss the state of the art of the underlying theories. Examples of most relevant experiments are also presented and discussed. Although not yet extensively investigated, the links between bulk rheology of foams and...
Article Chemical Reviews ; Volume 111, Issue 9 , June , 2011 , Pages 5610-5637 ; 00092665 (ISSN) ; Lynch, I ; Ejtehadi, M. R ; Monopoli, M. P ; Bombelli, F. B ; Laurent, S ; Sharif University of Technology
The significant role of protein nanoparticle interactions in nanomedicine and nanotoxicity is emerging recently through the identification of the nanoparticles (NP) protein (biomolecule) corona. The dynamic layer of proteins and/or other biomolecules adsorbed to the nanoparticle surface determines how a NP interacts with living systems and thereby modifies the cellular responses to the NP. Ehrenberg and co-workers used cultured endothelium cells as a model for vascular transport of polystyrene NP with various functional groups, which showed that the capacity of the various NP surfaces to adsorb proteins was indicative of their tendency to associate with cells. The quantification of the...
Utilization of molecular dynamics simulation coupled with experimental assays to optimize biocompatibility of an electrospun PCL/PVA scaffold, Article PLoS ONE ; Volume 12, Issue 1 , 2017 ; 19326203 (ISSN) ; Shamloo, A ; Mohseni, M ; Sharif University of Technology
Public Library of Science 2017
The main focus of this study is to address the possibility of using molecular dynamics (MD) simulation, as a computational framework, coupled with experimental assays, to optimize composite structures of a particular electrospun scaffold. To this aim, first, MD simulations were performed to obtain an initial theoretical insight into the capability of heterogeneous surfaces for protein adsorption. The surfaces were composed of six different blends of PVA (polyvinyl alcohol) and PCL (polycaprolactone) with completely unlike hydrophobicity. Next, MTT assay was performed on the electrospun scaffolds made from the same percentages of polymers as in MD models to gain an understanding of the...
PASylation enhances the stability, potency, and plasma half-life of interferon α-2a: A molecular dynamics simulation, Article Biotechnology Journal ; Volume 15, Issue 8 , 2020 ; Rostami, P ; Mahmoudi, A ; Sharif University of Technology
Wiley-VCH Verlag 2020
In this study, the effectiveness of PASylation in enhancing the potency and plasma half-life of pharmaceutical proteins has been accredited as an alternative technique to the conventional methods such as PEGylation. Proline, alanine, and serine (PAS) chain has shown some advantages including biodegradability improvement and plasma half-life enhancement while lacking immunogenicity or toxicity. Although some experimental studies have been performed to find the mechanism behind PASylation, the detailed mechanism of PAS effects on the pharmaceutical proteins has remained obscure, especially at the molecular level. In this study, the interaction of interferon α-2a (IFN) and PAS chain is...
Nano reengineering of horseradish peroxidase with dendritic macromolecules for stability enhancement, Article Enzyme and Microbial Technology ; Volume 50, Issue 1 , 2012 , Pages 10-16 ; 01410229 (ISSN) ; Vossoughi, M ; Shahrokhian, S ; Alemzadeh, I ; Sharif University of Technology
A simple bio-conjugation procedure to surround a single horseradish peroxidase (HRP) enzyme molecule with dendritic polyester macromolecules (polyester-32-hydroxyl-1-carboxyl bis-MPA dendron, generation 5) was proposed. The characterization of resultant nanoparticles entitled HRP dendrozyme, was performed by transmission electron microscopy, dynamic light scattering, gel permeation chromatography and Fourier transform infrared spectroscopy. The results showed that HRP nanoparticles were spherical in shape and have an average size of 14 ± 2. nm in diameter. Furthermore, bio-conformational characterization of HRP dendrozyme was performed by means of circular dichroism and fluorescence...
Article Channels ; Volume 11, Issue 3 , 2017 , Pages 209-223 ; 19336950 (ISSN) ; Bavi, O ; Vossoughi, M ; Naghdabadi, R ; Hill, A. P ; Martinac, B ; Jamali, Y ; Sharif University of Technology
Taylor and Francis Inc 2017
Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during...
Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study, Article Journal of Molecular Graphics and Modelling ; Volume 87 , 2019 , Pages 257-267 ; 10933263 (ISSN) ; Ghobeh, M ; Aghakhani Mahyari, F ; Rafii Tabar, H ; Sasanpour, P ; Sharif University of Technology
Elsevier Inc 2019
Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the...
Chaperones promote remarkable solubilization of salmonella enterica serovar enteritidis flagellin expressed in escherichia coli, Article Protein and Peptide Letters ; Volume 27, Issue 3 , 2020 , Pages 210-218 ; Sadeghi, Z ; Tarahomjoo, S ; Yaghmaie, S ; Sharif University of Technology
Bentham Science Publishers 2020
Background: Flagellin of Salmonella enterica serovar Enteritidis (SEF) stimulates immune responses to both itself and coapplied antigens. It is therefore used in vaccine development and immunotherapy. Removal of pathogenic S. enterica ser. Enteritidis from SEF production process is advantageous due to the process safety improvement. The protein solubility analysis using SDS-PAGE indicated that 53.49% of SEF expressed in Escherichia coli formed inclusion bodies. However, the protein recovery from inclusion bodies requires a complex process with a low yield. Objective: We thus aim to study possibility of enhancing SEF expression in E. coli in soluble form using chemical and molecular...