Theoretical-experimental studies of calmodulin-peptide interactions at different calcium equivalents.

abstract：:Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

journal_title：Journal of biomolecular structure & dynamics

authors： Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

更新日期：2020-07-31 00:00:00

abstract：:Human major histocompatibility complex class I (MHC I) - or human leukocyte antigen (HLA) - proteins present intracellularly processed peptides to cytotoxic T lymphocytes in the adaptive immune response to pathogens. A high level of polymorphism in human MHC I proteins defines the peptide-binding specificity of thousa...

journal_title：Journal of biomolecular structure & dynamics

authors： Serçinoğlu O,Ozbek P

更新日期：2018-02-01 00:00:00

abstract：:We previously reported on a mutant lipase KV1 (Mut-LipKV1) from Acinetobacter haemolyticus which optimal pH was raised from 8.0 to 11.0 after triple substitutions of surface aspartic acid (Asp) with lysine (Lys). Herein, this study further examined the Mut-LipKV1 by molecular docking, molecular dynamics (MD) simulatio...

journal_title：Journal of biomolecular structure & dynamics

authors： Anuar NFSK,Wahab RA,Huyop F,Amran SI,Hamid AAA,Halim KBA,Hood MHM

更新日期：2020-03-23 00:00:00

abstract：:Vibrio cholerae hemolysin (HlyA) is a 65 kDa pore-forming toxin which causes lysis of target eukaryotic cells by forming heptameric channels in the plasma membrane. Deletion of the 15 kDa C-terminus β-prism carbohydrate-binding domain generates a 50 kDa truncated variant (HlyA50) with 1000-fold-reduced pore-forming ac...

journal_title：Journal of biomolecular structure & dynamics

authors： Dutta S,Banerjee KK,Ghosh AN

更新日期：2014-01-01 00:00:00

abstract：:The drug design and discovery of lipid modulators is very demanding as no new molecule has entered into the market in the last 35 years. Cholesteryl ester transfer protein (CETP) is a promising target as lipid modulators. Inhibition of the CETP enzyme reduces the risk of cardiovascular events. The first CETP inhibitor...

journal_title：Journal of biomolecular structure & dynamics

authors： Amin SA,Adhikari N,Gayen S,Jha T

更新日期：2019-10-01 00:00:00

abstract：:In the present work fluctuations of number of ligands adsorbed on macromolecule are investigated. We have taken into account the adsorption and desorption of ligands under the circumstance of some adsorption centers fluctuations affected by medium fluctuation. The correlation function and spectral density of number of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arakelyan VB,Haroutiunian SG,Arakelyan HV,Haroutiunian TS

更新日期：2002-08-01 00:00:00

abstract：:Partial proteolysis of the lambda cI repressor has been carried out systematically with trypsin, chymotrypsin, elastase, endoproteinase Glu-C, kallikrein, and thrombin. The cleavage sites have been determined by (i) comparison of fragments produced and observed in SDS-polyacrylamide gel with known fragments and plots ...

journal_title：Journal of biomolecular structure & dynamics

authors： Pal A,Chattopadhyaya R

更新日期：2008-12-01 00:00:00

abstract：:Myo-inositol is one of the vital nutritional requirements for the Leishmania parasites' survival and virulence in the mammalian host. . Myo-inositol-1-phosphate synthase (MIPS) is responsible for the synthesis of myo-inositol in Leishmania, which plays a vital role in Leishmania's virulence to mammalian hosts. Earlier...

journal_title：Journal of biomolecular structure & dynamics

authors： Sinha M,Jagadeesan R,Kumar N,Saha S,Kothandan G,Kumar D

更新日期：2020-11-17 00:00:00

abstract：:Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-t...

journal_title：Journal of biomolecular structure & dynamics

authors： Boyarshin KS,Priss AE,Rayevskiy AV,Ilchenko MM,Dubey IY,Kriklivyi IA,Yaremchuk AD,Tukalo MA

更新日期：2017-02-01 00:00:00

abstract：:We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water-mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a prot...

journal_title：Journal of biomolecular structure & dynamics

authors： Mukherjee S,Nithin C,Divakaruni Y,Bahadur RP

更新日期：2019-03-01 00:00:00

abstract：:We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Benedetti G,Morosetti S

更新日期：1991-04-01 00:00:00

abstract：:Communicated by Ramaswamy H. Sarma. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Dubey S,Kallubai M,Subramanyam R

更新日期：2020-10-01 00:00:00

abstract：:We performed thermodynamic analysis of temperature-induced unfolding of mesophilic and thermophilic proteins. It was shown that the variability in protein thermostability associated with pH-dependent unfolding or linked to the substitution of amino acid residues on the protein surface is evidence of the governing role...

journal_title：Journal of biomolecular structure & dynamics

authors： Khechinashvili NN,Capital Ka Cyrillicabanov AV,Kondratyev MS,Polozov RV

更新日期：2014-01-01 00:00:00

abstract：:EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive 5-iodo-2'-deoxyuridine (i(5)dU) or 5-[4-(3-(trifl...

journal_title：Journal of biomolecular structure & dynamics

authors： Koudan EV,Subach OM,Korshunova GA,Romanova EA,Eritja R,Gromova ES

更新日期：2002-12-01 00:00:00

abstract：:The interaction of meso-tetra-(4N-oxyethylpyridyl)porphyrin (TOEPyP4) and its Zn(II)-, Cu(II)-, Mn(III)-derivatives with tRNA from E.Coli at low ionic strength (micro=0.02M) was studied using UV/Vis spectrophotometry and Circular Dichroism (CD) methods. An unusual Induced Circular Dichroism (ICD) spectra profile of th...

journal_title：Journal of biomolecular structure & dynamics

authors： Dalyan Y,Vardanyan I,Chavushyan A,Balayan G

更新日期：2010-08-01 00:00:00

abstract：:The EPR study of spin labeled macromolecules has provided insight into structural and dynamical properties of DNA, proteins, and related systems. While spin labeling has been useful, it is experimentally difficult to determine if the spin label significantly alters the conformation of the macromolecule to which it is ...

journal_title：Journal of biomolecular structure & dynamics

authors： Darian E,Gannett PM

更新日期：2005-04-01 00:00:00

abstract：:Tropomyosin receptor kinase A (Trk A) is a receptor tyrosine kinase activated by nerve growth factor (NGF). TrkA plays an important role in pain sensation, which leads to significant interest in the development of small molecule inhibitors of TrkA. However, TrkA and the other two highly homologous isoforms, TrkB and T...

journal_title：Journal of biomolecular structure & dynamics

authors： Wu X,Li Q,Wan S,Zhang J

更新日期：2021-01-01 00:00:00

abstract：:Ivermectin (IVM) is a broad-spectrum antiparasitic agent, having inhibitory potential against wide range of viral infections. It has also been found to hamper SARS-CoV-2 replication in vitro, and its precise mechanism of action against SARS-CoV-2 is yet to be understood. IVM is known to interact with host importin (IM...

journal_title：Journal of biomolecular structure & dynamics

authors： Azam F,Taban IM,Eid EEM,Iqbal M,Alam O,Khan S,Mahmood D,Anwar MJ,Khalilullah H,Khan MU

更新日期：2020-11-02 00:00:00

abstract：:The development of SrtA inhibitors targeting the biothreat organism namely Bacillus anthracis was achieved by the combined approach of pharmacophore modeling, binding interactions, electron transferring capacity, ADME, and Molecular dynamics studies. In this study, experimentally reported Ba-SrtA inhibitors (pyridazin...

journal_title：Journal of biomolecular structure & dynamics

authors： Selvaraj C,Singh SK

更新日期：2014-01-01 00:00:00

abstract：:Most β-Glucosidase (B8CYA8) are prone to inhibition by glucose. Experimentally observed specific activity of B8CYA8 on 20 mM, 50 mM, and 100 mM p-nitrophenyl-β-D-glucopyranoside (pNPGlc) substrate concentrations show surprise dependence on the presence of 0-3 M glucose at 335 K. We found that at high substrate concent...

journal_title：Journal of biomolecular structure & dynamics

authors： Konar S,Sinha SK,Datta S,Ghorai PK

更新日期：2020-07-28 00:00:00

abstract：:We report here two new small-size peptides acting as modulators of the β-site APP cleaving enzyme 1 (BACE1) exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderate but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initi...

journal_title：Journal of biomolecular structure & dynamics

authors： Gutierrez LJ,Angelina E,Gyebrovszki A,Fülöp L,Peruchena N,Baldoni HA,Penke B,Enriz RD

更新日期：2017-02-01 00:00:00

abstract：:Target evaluation is at the centre of rational drug design and biologics development. In order to successfully engineer antibodies, T-cell receptors or small molecules it is necessary to identify and characterise potential binding or contact sites on therapeutically relevant target proteins. Currently, there are numer...

journal_title：Journal of biomolecular structure & dynamics

authors： Kanapeckaitė A,Beaurivage C,Hancock M,Verschueren E

更新日期：2020-12-10 00:00:00

abstract：:The small ubiquitin-like modifier (SUMO) proteins are a kind of proteins that can be attached to a series of proteins. The sumoylation of protein is an important posttranslational modification. Thus, the prediction of the sumoylation site of a given protein is significant. Here we employed a combined method to perform...

journal_title：Journal of biomolecular structure & dynamics

authors： Cai Y,He J,Lu L

更新日期：2011-04-01 00:00:00

abstract：:Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...

journal_title：Journal of biomolecular structure & dynamics

authors： Quan Y,Xiong L,Chen J,Zhang HY

更新日期：2017-02-01 00:00:00

abstract：:Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenox...

journal_title：Journal of biomolecular structure & dynamics

authors： Rill RL,Marsch GA,Graves DE

更新日期：1989-12-01 00:00:00

abstract：:Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective se...

journal_title：Journal of biomolecular structure & dynamics

authors： Saha S,Bhattacharjee S,Chowdhury J

更新日期：2021-01-07 00:00:00

abstract：:The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...

journal_title：Journal of biomolecular structure & dynamics

authors： Fushman D,Ohlenschläger O,Rüterjans H

更新日期：1994-06-01 00:00:00

abstract：:The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at...

journal_title：Journal of biomolecular structure & dynamics

authors： Razavi L,Raissi H,Hashemzadeh H,Farzad F

更新日期：2020-06-05 00:00:00

abstract：:Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell-wall thickening. sHSP16.3 is also a promising candidate for vaccine, ser...

journal_title：Journal of biomolecular structure & dynamics

authors： Jee B,Kumar S,Yadav R,Singh Y,Kumar A,Sharma N

更新日期：2018-10-01 00:00:00

abstract：:Epidermal growth factor (EGF) plays important roles in multiple biological processes, such as the regulation of cell growth, proliferation, and differentiation. EGF exerts their pharmacologic effects via receptor-mediated mechanism associated with high affinity to epidermal growth factor receptor (EGFR) on the cell su...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehrabi M,Khodarahmi R,Shahlaei M

更新日期：2017-04-01 00:00:00