Molecular dynamics simulations of retinoblastoma protein.

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：:Owing to its negative regulatory role in insulin signaling, protein tyrosine phosphatase of leukocyte antigen-related protein (PTP-LAR) was widely thought as a potential drug target for diabetes. Now, it was urgent to search for potential LAR inhibitors targeting diabetes. Initially, the pharmacophore models of LAR in...

journal_title：Journal of biomolecular structure & dynamics

authors： Du S,Yang B,Wang X,Li WY,Lu XH,Zheng ZH,Ma Y,Wang RL

更新日期：2020-09-01 00:00:00

abstract：:Glutamine synthetase (GS) of Mycobacterium tuberculosis (Mtb) is an essential enzyme which is involved in nitrogen metabolism and cell wall synthesis. It is involved in the inhibition of phagosome-lysosome fusion by preventing acidification. Targeting GS can be helpful to control the infection of Mtb. In order to iden...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumari M,Subbarao N

更新日期：2020-10-01 00:00:00

abstract：:Three dimensional models of NB-ARC domains in five different proteins were constructed based on the recently published crystal structure of the apoptotic protease activating factor 1, of which two are for tomato species, one each for flax, Arabidopsis, and nematode. Standard multiple sequence alignment was performed f...

journal_title：Journal of biomolecular structure & dynamics

authors： Chattopadhyaya R,Pal A

更新日期：2008-02-01 00:00:00

abstract：:Sirtuin 2 is a key enzyme in gene expression regulation that is often associated with tumor proliferation control and therefore is a relevant anticancer drug target. Anilinobenzamide derivatives have been discussed as selective sirtuin 2 inhibitors and can be developed further. In the present study, hologram and three...

journal_title：Journal of biomolecular structure & dynamics

authors： Ferreira GM,Magalhães JG,Maltarollo VG,Kronenberger T,Ganesan A,Emery FDS,Trossini GHG

更新日期：2020-02-01 00:00:00

abstract：:Despite the intensive research efforts towards antiviral drug against COVID-19, no potential drug or vaccines has not yet discovered. Initially, the binding site of COVID-19 main protease was predicted which located between regions 2 and 3. Structure-based virtual screening was performed through a hierarchal mode of e...

journal_title：Journal of biomolecular structure & dynamics

authors： Mishra SS,Ranjan S,Sharma CS,Singh HP,Kalra S,Kumar N

更新日期：2020-07-15 00:00:00

abstract：:Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations show...

journal_title：Journal of biomolecular structure & dynamics

authors： Remin M

更新日期：1984-08-01 00:00:00

abstract：:The polymorphism exhibited by the mismatched octamer d(m5C-G-m5C-G-T-G-m5C-G), as a function of the temperature, DNA concentration and ionic strength, was investigated by means of NMR spectroscopy. It is shown that this partly self-complementary DNA fragment, under conditions of low DNA concentration (0.4 mM) and low ...

journal_title：Journal of biomolecular structure & dynamics

authors： Orbons LP,van der Marel GA,van Boom JH,Altona C

更新日期：1987-06-01 00:00:00

abstract：:Partition ratios of 8 free l-amino acids (Gln, Glu, His, Lys, Met, Ser, Thr, and Tyr) were measured in 10 different polymer/polymer aqueous two-phase systems containing 0.15 M NaCl in 0.01 M phosphate buffer, pH 7.4. The solute-specific coefficients representing the solute dipole/dipole, hydrogen-bonding and electrost...

journal_title：Journal of biomolecular structure & dynamics

authors： Madeira PP,Bessa A,Álvares-Ribeiro L,Raquel Aires-Barros M,Rodrigues AE,Uversky VN,Zaslavsky BY

更新日期：2014-01-01 00:00:00

abstract：:The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24...

journal_title：Journal of biomolecular structure & dynamics

authors： Andrianov AM

更新日期：1999-02-01 00:00:00

abstract：:Inhibition of heat shock protein 90 (Hsp90) is known to be a significantly effective strategy in cancer therapy. Here, pyrazolopyranopyrimidine derivatives were characterized as new Hsp90 inhibitors. The molecules' key structure (ZINC02819805) was determined by utilizing a pharmacophore model virtual screening workflo...

journal_title：Journal of biomolecular structure & dynamics

authors： Abbasi M,Amanlou M,Aghaei M,Bakherad M,Doosti R,Sadeghi-Aliabadi H

更新日期：2020-08-01 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：:Infections by Candida albicans in immune compromised patients cause significant morbidity and mortality. In the search for potential molecular targets for drug development, the family of agglutinin-like proteins (Als) in C. albicans have been identified due to numerous attributes associated with high virulence, most p...

journal_title：Journal of biomolecular structure & dynamics

authors： von Ranke NL,Bello ML,Cabral LM,Castro HC,Rodrigues CR

更新日期：2018-12-01 00:00:00

abstract：:The secondary structure of a bradykinin B(1)receptor antagonist B-10324 (F5C-Lys-(1)- Lys(0)-Arg(1)-Pro(2)- Hyp(3)-Gly(4)-CpG(5)- Ser(6)-DTic(7)-CpG(8)) was determined by NMR at 800MHz. The conformational data are compared with those obtained previously for two bradykinin B(1) receptor antagonists, namely B-9858 (Lys-...

journal_title：Journal of biomolecular structure & dynamics

authors： Miskolzie M,Gera L,Stewart JM,Kotovych G

更新日期：2002-02-01 00:00:00

abstract：:Previous research has described the interaction between the novel molecule diethidium (2,7-diamino 9-[2,7 diamino 10-N-phenanthridium] 10-N-phenanthridium) (Figure 1) and B-form DNA. Our goal is the elucidation of diethidium as the first member of a novel class of drugs which are potential pharmaceutical agents. This ...

journal_title：Journal of biomolecular structure & dynamics

authors： Monaco RR,Polkosnik W,Dwarakanath S

更新日期：1997-08-01 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：:All major suggestions about the nucleosome positioning sequence pattern(s) are overviewed. Two basic binary periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR and in strong/weak alphabet -SWWWWWSSSSSW. Their merger in four-letter alphabet sequence coincides with first ever complete ...

journal_title：Journal of biomolecular structure & dynamics

authors： Trifonov EN

更新日期：2010-06-01 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：:The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechan...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets' OO,Hovorun DM

更新日期：2015-01-01 00:00:00

abstract：:Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran-PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of...

journal_title：Journal of biomolecular structure & dynamics

authors： Ferreira LA,Povarova OI,Stepanenko OV,Sulatskaya AI,Madeira PP,Kuznetsova IM,Turoverov KK,Uversky VN,Zaslavsky BY

更新日期：2017-01-01 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：:2019 - Novel Coronavirus (2019-nCOV), enclosed large genome positive-sense RNA virus characterized by crown-like spikes that protrude from their surface, and have a distinctive replication strategy. The 2019-nCOV belongs to the Coronaviridae family, principally consists of virulent pathogens showing zoonotic property,...

journal_title：Journal of biomolecular structure & dynamics

authors： Naik VR,Munikumar M,Ramakrishna U,Srujana M,Goudar G,Naresh P,Kumar BN,Hemalatha R

更新日期：2020-06-22 00:00:00

abstract：:We study the CaM-peptide interactions for four CaM-related peptides with different calcium equivalents, using the hCaM-M124C-mBBr biosensor and Molecular Dynamics (MD). Due to the high sensitivity of the biosensor, we were able to calculate five Kds based on the number of calcium equivalents for each peptide, showing ...

journal_title：Journal of biomolecular structure & dynamics

authors： Sosa-Peinado A,León-Cruz E,Velázquez-López I,Matuz-Mares D,Cano-Sánchez P,González-Andrade M

更新日期：2020-10-30 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：: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：:The reproducibility of melting curves for repeated hybridizations of target DNA with generic oligonucleotide microchips is shown experimentally to depend on the character of matching between fragments of target DNA and immobilized oligonucleotides. The reproducibility of melting curves is higher for the perfect match ...

journal_title：Journal of biomolecular structure & dynamics

authors： Lebed JB,Chechetkin VR,Turygin AY,Shick VV,Mirzabekov AD

更新日期：2001-06-01 00:00:00

abstract：:An extensive Monte Carlo simulation of hydration of various conformations of the dinucleoside monophosphates (DNP), containing thymine, uracil and its 5-halogen derivatives has been performed. An anti-anti conformation is the most energetically stable one for each of the DNPs. In the majority of cases the energy prefe...

journal_title：Journal of biomolecular structure & dynamics

authors： Alderfer JL,Danilov VI,Poltev VI,Slyusarchuk ON

更新日期：1999-04-01 00:00:00

abstract：:The knowledge of the relationship between the three-dimensional structure of a protein and its biological and stability is one of the most challenging problem in protein chemistry, since offers the possibility of changing both the specific action of a protein and its stability. In this work, we have approached the pro...

journal_title：Journal of biomolecular structure & dynamics

authors： Pedone EM,Bartolucci S,Rossi M,Saviano M

更新日期：1998-10-01 00:00:00

abstract：:Most fibrous polynucleotides of general sequence exhibit secondary structures that are described adequately by regular helices with a repeated motif of only one nucleotide. Such helices exploit the fact that A:T, T:A, G:C, and C:G pairs are essentially isomorphous and have dyadically-related glycosylic bonds. Polynucl...

journal_title：Journal of biomolecular structure & dynamics

authors： Arnott S,Chandrasekaran R,Banerjee AK,He R,Walker JK

更新日期：1983-10-01 00:00:00

abstract：:The crystal-state preferred conformation of the terminally blocked hepta- and octapeptides with the general formula -(Aib)n L-Leu-(Aib)2- (n = 4 and 5, respectively), determined by X-ray diffraction, was found to be a right-handed 3(10)-helix stabilized by five and six consecutive intramolecular NH...O = C H-bonds of ...

journal_title：Journal of biomolecular structure & dynamics

authors： Bavoso A,Benedetti E,Di Blasio B,Pavone V,Pedone C,Toniolo C,Bonora GM,Formaggio F,Crisman M

更新日期：1988-02-01 00:00:00