Conformational space comparison of GnRH and lGnRH-III using molecular dynamics, cluster analysis and Monte Carlo thermodynamic integration.

abstract：:Fpg protein (formamidopyrimidine or 8-oxoguanine DNA glycosylase) from E. coli catalyzes excision of several damaged purine bases, including 8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine from DNA. In this study the interaction of E. coli Fpg with various specific and nonspecific oligodeoxynucleo...

journal_title：Journal of biomolecular structure & dynamics

authors： Ishchenko AA,Koval VV,Fedorova OS,Douglas KT,Nevinsky GA

更新日期：1999-10-01 00:00:00

abstract：:The specific interaction between lambda phage Cro repressor and the DNA fragment bearing the consensus sequence of operators has been studied using nuclear magnetic resonance (NMR). Using both 15N- and 13C/15N- labeled lambda-Cro in complex with unlabeled DNA, chemical shift assignments of the lambda-Cro-DNA complex w...

journal_title：Journal of biomolecular structure & dynamics

authors： Tochio H,Kojima C,Matsuo H,Yamazaki T,Kyogoku Y

更新日期：1999-04-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Khan S,Somvanshi P,Singh A,Khan M,Mandal RK,Dar SA,Wahid M,Jawed A,Mishra BN,Haque S

更新日期：2020-03-03 00:00:00

abstract：:Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergenc...

journal_title：Journal of biomolecular structure & dynamics

authors： Costa Júnior DB,Araújo JSC,de Mattos Oliveira L,Neri FSM,Moreira POL,Taranto AG,Fonseca AL,de Pilla Varotti F,Leite FHA

更新日期：2020-05-13 00:00:00

abstract：:Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploit...

journal_title：Journal of biomolecular structure & dynamics

authors： Patel A,Tiwari S,Jha PK

更新日期：2019-04-01 00:00:00

abstract：:Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sharmila DJ,Veluraja K

更新日期：2006-06-01 00:00:00

abstract：:Ebola virus (EboV) is currently ravaging West Africa with estimated case fatality rate of 52%. Currently, no drug treatment is available and immunoglobulin therapy is still at the rudimentary stage. For anti-EboV drug development, druggable viral and host protein targets, including human Furin are under intense invest...

journal_title：Journal of biomolecular structure & dynamics

authors： Omotuyi IO

更新日期：2015-01-01 00:00:00

abstract：:Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...

journal_title：Journal of biomolecular structure & dynamics

authors： Dhal AK,Pani A,Yun SI,Mahapatra RK

更新日期：2020-07-07 00:00:00

abstract：:Mycobacterium tuberculosis remains one of the most successful bacterial pathogens worldwide. The development of drug-resistant strains and the ability of the bacteria to persist in a latent form in the host are major problems for tuberculosis (TB) control. Glyoxylate shunt is a metabolic bypass of the Krebs cycle and ...

journal_title：Journal of biomolecular structure & dynamics

authors： Shukla R,Shukla H,Tripathi T

更新日期：2020-04-30 00:00:00

abstract：:Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.gya...

journal_title：Journal of biomolecular structure & dynamics

authors： Das S,Mukherjee R,Sahoo S,Thakkar R,Chakrabarti J

更新日期：2009-12-01 00:00:00

abstract：:Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undec...

journal_title：Journal of biomolecular structure & dynamics

authors： Laberge M,Vreugdenhil AJ,Vanderkooi JM,Butler IS

更新日期：1998-06-01 00:00:00

abstract：:The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25-30 residues. 3D structural RMSD comparisons of the closed loops and presentati...

journal_title：Journal of biomolecular structure & dynamics

authors： Frenkel ZM,Trifonov EN

更新日期：2005-06-01 00:00:00

abstract：:In order to examine whether chiral metal complexes can be used to discriminate between right- and left-handed DNA conformational states we have studied the enantioselective interactions of Fe(phen)3(2+) and Ru(phen)3(2+) (phen = 1,10-phenanthroline) with poly(dGm5dC) under B- and Z-form conditions. With the inversion-...

journal_title：Journal of biomolecular structure & dynamics

authors： Härd T,Hiort C,Nordén B

更新日期：1987-08-01 00:00:00

abstract：:Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...

journal_title：Journal of biomolecular structure & dynamics

authors： Malkhed V,Mustyala KK,Potlapally SR,Vuruputuri U

更新日期：2014-12-01 00:00:00

abstract：:Base sequence effects within double stranded RNA oligomers of A and Z conformations have been studied by molecular modeling using a methodological approach specifically adapted to nucleic acids. Calculations on symmetric oligomers having homonucleotide or dinucleotide repeating base sequences show that sequence change...

journal_title：Journal of biomolecular structure & dynamics

authors： Hartmann B,Lavery R

更新日期：1989-10-01 00:00:00

abstract：:Human β-defensin-3 (HβD-3) is an endogenous antimicrobial peptide with potent and broad killing activity against various microorganisms, and thus, it is an attractive candidate for the development of novel peptide antibiotics, but its antimicrobial mechanism remains elusive. To characterize the mechanism, we used mult...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao X,Yu H,Yang L,Li Q,Huang X

更新日期：2015-01-01 00:00:00

abstract：:Malaria is still one of the deadly diseases resulting in deaths of millions of people worldwide and situation has become worse due to alarming rise in anti-malarial drug resistance. Genome sequence availability of Plasmodium falciparum, the main causal organism of severe malaria in humans, has enabled identification o...

journal_title：Journal of biomolecular structure & dynamics

authors： Kaushik A,Subramaniam S,Gupta D

更新日期：2014-01-01 00:00:00

abstract：:A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are succes...

journal_title：Journal of biomolecular structure & dynamics

authors： Jaumot J,Aviña A,Eritja R,Tauler R,Gargallo R

更新日期：2003-10-01 00:00:00

abstract：:In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the seco...

journal_title：Journal of biomolecular structure & dynamics

authors： Seshadri K,Rao VS,Vishveshwara S

更新日期：1994-12-01 00:00:00

abstract：:HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on th...

journal_title：Journal of biomolecular structure & dynamics

authors： Triki D,Kermarrec M,Visseaux B,Descamps D,Flatters D,Camproux AC,Regad L

更新日期：2020-10-01 00:00:00

abstract：:Triple-negative breast cancers (TNBCs) are one of the most aggressive and complex forms of cancers in women. TNBCs are commonly known for their complex heterogeneity and poor prognosis. The present work aimed to develop a predictive 2D and 3D quantitative structure-activity relationship (QSAR) models against metastati...

journal_title：Journal of biomolecular structure & dynamics

authors： Shukla A,Tyagi R,Meena S,Datta D,Srivastava SK,Khan F

更新日期：2020-01-01 00:00:00

abstract：:Molecular modeling and molecular dynamics were performed to investigate the interaction of norfloxacin with the DNA oligonucleotide 5'-d(ATACGTAT)(2). Eight quinolone-DNA binding structures were built by molecular modeling on the basis of experimental results. A 100ps molecular dynamics calculation was carried out on ...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee HM,Kim JK,Kim SK

更新日期：2002-06-01 00:00:00

abstract：:It is generally believed that base-pair stacking interaction in DNA double helix is one of the strongest interactions that governs sequence directed structural variability. However, X-ray crystal structures of some base-paired doublet sequences have been seen to adopt different structures when flanked by different bas...

journal_title：Journal of biomolecular structure & dynamics

authors： Bandyopadhyay D,Bhattacharyya D

更新日期：2000-08-01 00:00:00

abstract：:The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four s...

journal_title：Journal of biomolecular structure & dynamics

authors： Fernandes CL,Escouto GB,Verli H

更新日期：2014-01-01 00:00:00

abstract：:Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials hav...

journal_title：Journal of biomolecular structure & dynamics

authors： Lee SA,Pinnick DA,Anderson A

更新日期：2015-01-01 00:00:00

abstract：:Human C5a (hC5a), one of the pro-inflammatory glycoproteins of the complement system is known to undergo production hyperdrive in response to stress and infection. hC5a has been associated with the pathogenesis of many chronic and acute diseases, due to its proven ability in triggering the 'cytokine storm', by binding...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra R,Behera LM,Rana S

更新日期：2020-09-15 00:00:00

abstract：:The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each...

journal_title：Journal of biomolecular structure & dynamics

authors： Haasnoot CA,Westerink HP,van der Marel GA,van Boom JH

更新日期：1984-10-01 00:00:00

abstract：:We have examined the conformational energetics of the eight most commonly occurring nucleosides--A, U, G, C, dA, dT, dG, dC--as monitored by a semi-empirical energy force field. These are the first reported calculations to completely explore the entire conformational spaces available to all eight major nucleosides usi...

journal_title：Journal of biomolecular structure & dynamics

authors： Pearlman DA,Kim SH

更新日期：1985-08-01 00:00:00

abstract：:Thorough quantitative study of nucleosome repeat length (NRL) distributions, conducted in 1992 by J. Widom, resulted in a striking observation that the linker lengths between the nucleosomes are quantized. Comparison of the NRL average values with the MNase cut distances predicted from the hypothetical columnar struct...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2016-06-01 00:00:00

abstract：:Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distributio...

journal_title：Journal of biomolecular structure & dynamics

authors： Beveridge DL,Maye PV,Jayaram B,Ravishanker G,Mezei M

更新日期：1984-10-01 00:00:00