Dynamical study, hydrogen bond analysis, and constant pH simulations of the beta carbonic anhydrase of Methanobacterium thermoautotrophicum.

abstract：:Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buc...

journal_title：Journal of biomolecular structure & dynamics

authors： Danilov VI,Anisimov VM

更新日期：2005-02-01 00:00:00

abstract：:Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions...

journal_title：Journal of biomolecular structure & dynamics

authors： Shchelkanov MYu,Starikov NS,Yaroslavtsev IV,Tsvetkov PO,Yudin AN,Denisov MV,Slavsky AA,Vedenov AA,Karamov EV

更新日期：1998-04-01 00:00:00

abstract：:Oligonucleotides containing 1-(beta-D-2'-deoxy-threo-pentofuranosyl)cytosine (dCx) and/or 1-(beta-D-2'-deoxy-threo-pentofuranosyl)thymine (dTx) in place of dC and dT residues in the EcoRII and MvaI recognition site CC(A/T)GG were synthesized in order to investigate specific recognition of the DNA sugar-phosphate backb...

journal_title：Journal of biomolecular structure & dynamics

authors： Petrauskene OV,Yakovleva JN,Alekseev YI,Subach FV,Babkina OV,Gromova ES

更新日期：2000-04-01 00:00:00

abstract：:P2Y12 receptor is an attractive target for the anti-platelet therapies, treating various thrombotic diseases. In this work, a total of 107 6-aminonicotinate-based compounds as potent P2Y12 antagonists were studies by a molecular modeling study combining three-dimensional quantitative structure-activity relationship (3...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhou S,Fang D,Tan S,Lin W,Wu W,Zheng K

更新日期：2017-10-01 00:00:00

abstract：:Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosid...

journal_title：Journal of biomolecular structure & dynamics

authors： Mondragon-Sanchez JA,Liquier J,Shafer RH,Taillandier E

更新日期：2004-12-01 00:00:00

abstract：:The purpose of this study was to investigate the site-selective binding of erlotinib hydrochloride (ET), a targeted anticancer drug, to bovine serum albumin (BSA) through 1H NMR, spectroscopic, thermodynamic, and molecular modeling methods. The fluorescence quenching of BSA by ET was a result of the formation of BSA-E...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu Y,Chen M,Luo Z,Lin J,Song L

更新日期：2013-10-01 00:00:00

abstract：:The N-terminal receiver domain of NtrC is the molecular switch in the two-component signal transduction. It is the first protein where structures of both the active (phosphyroylated) and inactive (unphosphyroylated) states are determined experimentally. Phosphorylation of the NtrC at the active site induces large stru...

journal_title：Journal of biomolecular structure & dynamics

authors： Hu X,Wang Y

更新日期：2006-04-01 00:00:00

abstract：:Mutations of any subunit of the troponin complex may lead to serious disorders. Rational approaches to managing these disorders require knowledge of the complex interactions among the three subunits that are required for proper function. Molecular dynamics (MD) simulations were performed for both skeletal (sTn) and ca...

journal_title：Journal of biomolecular structure & dynamics

authors： Varughese JF,Chalovich JM,Li Y

更新日期：2010-10-01 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 binding of the anilido aminoacridine derivative amsacrine with the heme proteins, hemoglobin, and myoglobin, was characterized by various spectroscopic and calorimetric methods. The binding affinity to hemoglobin was (1.21 ± .05) × 105 M-1, while that to myoglobin was three times higher (3.59 ± .15) × 105 M-1. The...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhowmik D,Suresh Kumar G

更新日期：2017-05-01 00:00:00

abstract：:A molecular dynamics simulation of the Sm binding site from human U4 snRNA was undertaken to determine the conformational flexibility of this region and to identify RNA conformations that were important for binding of the Sm proteins. The RNA was fully-solvated (>9,000 water molecules) and charge neutralized by inclus...

journal_title：Journal of biomolecular structure & dynamics

authors： Guo J,Daizadeh I,Gmeiner WH

更新日期：2000-12-01 00:00:00

abstract：:Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived muta...

journal_title：Journal of biomolecular structure & dynamics

authors： Ramakrishnan C,Subramanian V,Balamurugan K,Velmurugan D

更新日期：2013-01-01 00:00:00

abstract：:In order to investigate the interfacial activation of a lipase from Pseudomonas cepacia (PcL), molecular dynamics (MD) simulations and essential dynamics (ED) analysis were performed in different solvent environments: vacuum and explicit water solvents. Starting from the active (open) structure of PcL, the essential d...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee J,Suh SW,Shin S

更新日期：2000-10-01 00:00:00

abstract：:Homologous proteins may fold into similar three-dimensional structures. Spectroscopic evidence suggests this is true for the cereal grain thionins, the mistletoe toxins, and for crambin, three classes of plant proteins. We have combined primary sequence homology and energy minimization to predict the structures alpha ...

journal_title：Journal of biomolecular structure & dynamics

authors： Whitlow M,Teeter MM

更新日期：1985-02-01 00:00:00

abstract：:Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...

journal_title：Journal of biomolecular structure & dynamics

authors： Murphy D,Doyle H,Eritja R,Redmond G

更新日期：2004-10-01 00:00:00

abstract：:Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in the tobacco plant both remote leaf necrosis and the induction of a resistance against subsequent attack by various micro-organisms. The crystal structure of b-cryptogein (CRY), secreted by Phytophthora cryptogea, was previou...

journal_title：Journal of biomolecular structure & dynamics

authors： Demaret S,Demaret JP,Brunie S

更新日期：2000-12-01 00:00:00

abstract：:NMR experiments with a 21412 Redfield observation pulse were carried out on a kappa-carrageenan aqueous solution containing 0.5M LiI. A detected hydrogen-bonded proton resonance at approximately 17.6 ppm, is in accordance with an ordered carrageenan structure in the solution similar to the double, parallel-stranded he...

journal_title：Journal of biomolecular structure & dynamics

authors： Nerdal W,Haugen F,Knutsen S,Grasdalen H

更新日期：1993-04-01 00:00:00

abstract：:The SARS-CoV-2 is the causative agent of COVID-19 pandemic that is causing a global health emergency. The lack of targeted therapeutics and limited treatment options have triggered the scientific community to develop new vaccines or small molecule therapeutics against various targets of SARS-CoV-2. The main protease (...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhardwaj VK,Singh R,Sharma J,Rajendran V,Purohit R,Kumar S

更新日期：2020-05-20 00:00:00

abstract：:Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Berger I,Spačková N,Leszczynski J,Hobza P

更新日期：2000-01-01 00:00:00

abstract：:Tau-tubulin kinase 1 inhibitors inhibit tau protein phosphorylation on Ser198, Ser199, Ser202, Ser422, and also in paired helical filaments. We developed receptor-based pharmacophore models by exploiting three TTBK1 protein structures, i.e., 4NFN, 4BTM, and 4BTK. The integrated e-pharmacophore based virtual screening ...

journal_title：Journal of biomolecular structure & dynamics

authors： Jana S,Singh SK

更新日期：2020-02-01 00:00:00

abstract：:Proteins are nature's biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for their macro-scaled counterparts, convert (part of) other/various...

journal_title：Journal of biomolecular structure & dynamics

authors： Gur M,Golcuk M,Yilmaz SZ,Taka E

更新日期：2020-02-01 00:00:00

abstract：:Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning-based AutoQSAR algorithm to generate drug leads for the flaviviruses-Dengue and West Nile. The drug leads generated by the program are fed as programmatic inputs to AutoDock Vina package for...

journal_title：Journal of biomolecular structure & dynamics

authors： Geoffrey B,Sanker A,Madaj R,Tresanco MSV,Upadhyay M,Gracia J

更新日期：2020-12-04 00:00:00

abstract：:Abstract The stacking preference of a DNA Four-Way junction (4H), with a novel junction sequence, has been determined in the presence of magnesium ions as well as in the presence of cobalt(III)hexammine ions by means of NMR spectroscopy. In both cases this 4H has a strong preference (>80%) to fold in an A/D-stacked ...

journal_title：Journal of biomolecular structure & dynamics

authors： van Buuren BN,Schleucher J,Wijmenga SS

更新日期：2000-01-01 00:00:00

abstract：:Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...

journal_title：Journal of biomolecular structure & dynamics

authors： Dai H,McFarland EW

更新日期：1996-04-01 00:00:00

abstract：:Diabetes is very much known as a wide-spread disorder all around the world with serious complications for the diabetic patient. In order to reduce these complications, inhibition the activity of aldose reductase (AR) and cyclooxygenase-2 (COX-2) enzymes is a proposed pathway. Within this work potency of curcumin (CUR)...

journal_title：Journal of biomolecular structure & dynamics

authors： Mirzaei M,Harismah K,Soleimani M,Mousavi S

更新日期：2020-07-31 00:00:00

abstract：:Acinetobacter baumannii, an important nosocomial pathogen, is increasingly becoming resistant to antibiotics including recent β-lactam like imipenem. Production of different types of β-lactamases is one of the major resistance mechanisms which bacteria adapt. We recently reported the presence of a β-lactamase, OXA-51,...

journal_title：Journal of biomolecular structure & dynamics

authors： Tiwari V,Moganty RR

更新日期：2014-01-01 00:00:00

abstract：:A complete three dimensional model (RCSB000408; PDB code 1qaa) for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor is proposed. A model of interaction of the N-terminal operator binding domain 1-72 with the operator was available. We ...

journal_title：Journal of biomolecular structure & dynamics

authors： Chattopadhyaya R,Ghosh K,Namboodiri VM

更新日期：2000-10-01 00:00:00

abstract：:Among the plant constituents of Clerodendrum colebrookianum Walp., acteoside, martinoside, and osmanthuside β6 interact with ROCK, a drug target for cancer. In this study, aglycone fragments of these plant constituents (caffeic acid, ferulic acid, and p-coumaric acid) along with the homopiperazine ring of fasudil (sta...

journal_title：Journal of biomolecular structure & dynamics

authors： Arya H,Yadav CS,Lin SY,Syed SB,Charles MRC,Kannadasan S,Hsieh HP,Singh SS,Gajurel PR,Coumar MS

更新日期：2020-08-01 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：:The worldwide expanding increment in cancer pervasiveness is disturbing and this disease ranks among the main causes of mortality in both developing and developed countries. Unfortunately, available treatment options come with serious side effects and do not guarantee complete success. Although numerous models have be...

journal_title：Journal of biomolecular structure & dynamics

authors： Ojo OA,Aruleba RT,Adekiya TA,Sibuyi NRS,Ojo AB,Ajiboye BO,Oyinloye BE,Adeola HA,Fadaka AO

更新日期：2020-09-14 00:00:00