DNA binding by TATA-box binding protein (TBP): a molecular dynamics computational study.

abstract：:The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from natural plant sources is an area of immense potential. The curre...

journal_title：Journal of biomolecular structure & dynamics

authors： Wahedi HM,Ahmad S,Abbasi SW

更新日期：2020-05-12 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：:Bruton's tyrosine kinase (Btk) is an important enzyme in B-lymphocyte development and differentiation. Furthermore, Btk expression is considered essential for the proliferation and survival of these cells. Btk inhibition has become an attractive strategy for treating autoimmune diseases, B-cell leukemia, and lymphomas...

journal_title：Journal of biomolecular structure & dynamics

authors： Santos-Garcia L,Assis LC,Silva DR,Ramalho TC,da Cunha EF

更新日期：2016-07-01 00:00:00

abstract：:Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen bonded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To ch...

journal_title：Journal of biomolecular structure & dynamics

authors： Kiran MR,Bansal M

更新日期：1998-12-01 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

abstract：:Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorptio...

journal_title：Journal of biomolecular structure & dynamics

authors： Roy A,Seal P,Sikdar J,Banerjee S,Haldar R

更新日期：2018-02-01 00:00:00

abstract：:The SHOM method (Sequencing by Hybridization with Oligonucleotide Matrix) developed in 1988 is a new approach to nucleic acid sequencing by hybridization to an oligonucleotide matrix composed of an array of immobilized oligonucleotides. The original matrix proposed for sequencing by SHOM had to contain at least 65,536...

journal_title：Journal of biomolecular structure & dynamics

authors： Pevzner PA,Lysov YuP,Khrapko KR,Belyavsky AV,Florentiev VL,Mirzabekov AD

更新日期：1991-10-01 00:00:00

abstract：:In negatively supercoiled DNA molecules some inverted repeat sequences adopt a perturbed conformation which is characterised by the following properties. They are centrally hypersensitive to single-strand-specific nucleases such as S1, and to a much lower extent the flanking regions may also be sensitive. They are als...

journal_title：Journal of biomolecular structure & dynamics

authors： Lilley DM,Hallam LR

更新日期：1983-10-01 00:00:00

abstract：:We have developed an iterative hybrid algorithm (HA) to predict the 3D structure of peptides starting from their amino acid sequence. The HA is made of a modified genetic algorithm (GA) coupled to a local optimizer. Each HA iteration is carried out in two phases. In the first phase several GA runs are performed upon t...

journal_title：Journal of biomolecular structure & dynamics

authors： Garduño-Juárez R,Morales LB

更新日期：2003-08-01 00:00:00

abstract：:The location, orientation and dynamics of a thiazole-containing analogue of distamycin 1 bound to the decadeoxyribonucleotide d-[CGCAATTGCG]2 have been studied by non-exchangable and imino proton NMR resonances of the 1:1 complex. Using NOE difference, COSY and NOESY experiments, lexitropsin (1) was located in the min...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar S,Bathini Y,Joseph T,Pon RT,Lown JW

更新日期：1991-08-01 00:00:00

abstract：:Repetitive basic polypeptides containing lysine or arginine as every third amino acid were shown to cause DNA condensation at physiological salt concentration connected with selective DNA binding with respect to DNA composition and sequence. This selectivity is very similar to that existing in the case of histone H1 a...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponar J,Votavová H

更新日期：1996-06-01 00:00:00

abstract：:The viral cathepsin from Bombyx mori Nuclear Polyhedrosis Virus (BmNPV-Cath) is a broad-spectrum protease that participates in the horizontal transmission of this virus in silkworm by facilitating solubilization of the integument of infected caterpillars. When a B. mori farm is attacked by BmNPV, there are significant...

journal_title：Journal of biomolecular structure & dynamics

authors： Sérgio Alves Bueno P,Carina Biavatti D,Sandro Gularte Chiarello A,Aureliana Fassina V,Aparecida Fernandez M,Augusto Vicente Seixas F

更新日期：2019-09-01 00:00:00

abstract：:The subtype, 5-HT7R has been implicated in neurological disorders and presents itself as a promising target for antidepressant drugs. Design of targeted selective ligands, require a sound knowledge of 3D-receptor structure. In absence of receptor structure, structure-based design of targeted ligands relies on generati...

journal_title：Journal of biomolecular structure & dynamics

authors： Jha P,Chaturvedi S,Swastika,Pal S,Jain N,Mishra AK

更新日期：2018-08-01 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：:Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Fo...

journal_title：Journal of biomolecular structure & dynamics

authors： Bathaie SZ,Ajloo D,Daraie M,Ghadamgahi M

更新日期：2015-01-01 00:00:00

abstract：:The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of α...

journal_title：Journal of biomolecular structure & dynamics

authors： Anwer K,Sonani R,Madamwar D,Singh P,Khan F,Bisetty K,Ahmad F,Hassan MI

更新日期：2015-01-01 00:00:00

abstract：:Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Patel HM,Shaikh M,Ahmad I,Lokwani D,Surana SJ

更新日期：2020-04-23 00:00:00

abstract：:P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

journal_title：Journal of biomolecular structure & dynamics

authors： Yellapu NK,Pulaganti M,Pakala SB

更新日期：2017-08-01 00:00:00

abstract：:The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and...

journal_title：Journal of biomolecular structure & dynamics

authors： Cao Z,Liu L,Wang J

更新日期：2010-12-01 00:00:00

abstract：:The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human ...

journal_title：Journal of biomolecular structure & dynamics

authors： Santhiya P,Christian Bharathi A,Syed Ibrahim B

更新日期：2020-09-01 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 unavailability of vaccine and medicines raised serious issues during COVID-19 pandemic and peoples from different parts of world relied on traditional medicine for their immediate recovery from COVID-19 and it found effective also. The current research aims to target COVID-19 immunological human host receptors i.e...

journal_title：Journal of biomolecular structure & dynamics

authors： Noor H,Ikram A,Rathinavel T,Kumarasamy S,Nasir Iqbal M,Bashir Z

更新日期：2021-01-25 00:00:00

abstract：:We have analysed S1 sensitivity of SV40 minichromosomes isolated from the nuclei of infected cells at the late stage of infection. We show that a fraction of purified minichromosomes is sensitive towards double-strand cleavage by S1 nuclease. The pattern of specific cleavage reminiscent of that found for subcloned fra...

journal_title：Journal of biomolecular structure & dynamics

authors： Nedospasov SA,Shakhov AN,Hirt B

更新日期：1989-04-01 00:00:00

abstract：:The superoxide-generating activity of Nox5 is regulated by Ca2+ flux, primarily through its self-contained calcium binding domain (EFD). Upon Ca2+ binding, Nox5's EFD undergoes a conformational change that exposes its buried hydrophobic residues. Previously, we determined the Ca2+ binding constants of the N-terminal h...

journal_title：Journal of biomolecular structure & dynamics

authors： Wei CC,Fabry E,Hay E,Lloyd L,Kaufman N,Yang YP,Stuehr DJ

更新日期：2020-05-01 00:00:00

abstract：:COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to co...

journal_title：Journal of biomolecular structure & dynamics

authors： Swargiary A,Mahmud S,Saleh MA

更新日期：2020-10-22 00:00:00

abstract：:Doublesex and Mab-3-related transcription factor (DMRT) gene family is widely known for its involvement in sex determination and/or differentiation among different phyla. In this study, we identify eight DMRT genes in the cephalochordate amphioxus, a protochordate holding a key phylogenetic position. The eight DMRTs c...

journal_title：Journal of biomolecular structure & dynamics

authors： Wang F,Yu Y,Ji D,Li H

更新日期：2012-01-01 00:00:00

abstract：:The conformational space available to GnRH and lGnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calcu...

journal_title：Journal of biomolecular structure & dynamics

authors： Watts CR,Mezei M,Murphy RF,Lovas S

更新日期：2001-04-01 00:00:00

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

journal_title：Journal of biomolecular structure & dynamics

authors： Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

更新日期：2020-11-06 00:00:00

abstract：:Distinction criterion for various sets of fixed length peptide fragments and integral distinction measure for various sets of peptide fragments with different length and start position ranges have been introduced on the base of an enumeration procedure and a point estimators for the amino acid distribution characteris...

journal_title：Journal of biomolecular structure & dynamics

authors： Shchelkanov MYu,Starikov NS,Yaroslavtsev IV,Yudin AN,Antonov AV,Novak IL,Vedenov AA,Karamov EV

更新日期：1997-12-01 00:00:00

abstract：:The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhavnani V,Kaviraj S,Panigrahi P,Suresh CG,Yapara S,Pal J

更新日期：2018-08-01 00:00:00