Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

abstract：:Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes...

journal_title：Journal of biomolecular structure & dynamics

authors： Chen L,Yang J,Huang T,Kong X,Lu L,Cai YD

更新日期：2016-01-01 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：:The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...

journal_title：Journal of biomolecular structure & dynamics

authors： Bashford D,Weaver DL,Karplus M

更新日期：1984-03-01 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 sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation...

journal_title：Journal of biomolecular structure & dynamics

authors： Pastor N,MacKerell AD Jr,Weinstein H

更新日期：1999-02-01 00:00:00

abstract：:The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is...

journal_title：Journal of biomolecular structure & dynamics

authors： Vondrásek J,Sponar J,Hobza P

更新日期：1994-02-01 00:00:00

abstract：:Two aminobenzoic acid derivatives DAB-0 and DAB-1 showed distinct biological properties on murine bladder cancer (BCa) cell line MB49-I. In contrast to DAB-1, DAB-0 does not possess any anti-inflammatory activity and is less toxic. Furthermore, DAB-0 does not interfere with INFγ-induced STAT1 activation and TNFα-induc...

journal_title：Journal of biomolecular structure & dynamics

authors： Chanphai P,Cloutier F,Oufqir Y,Leclerc MF,Eiján AM,Reyes-Moreno C,Bérubé G,Tajmir-Riahi HA

更新日期：2021-01-01 00:00:00

abstract：:Coumarin molecules have biological activities possessing lipid-controlling activity, anti-hepatitis C activity, anti-diabetic, anti-Parkinson activity, and anti-cancer activity. Here, we have presented an inclusive study on the interaction of 8-substituted-7-hydroxy coumarin derivatives (Umb-1/Umb-2) with α-1-glycopro...

journal_title：Journal of biomolecular structure & dynamics

authors： Yeggoni DP,Manidhar DM,Suresh Reddy C,Subramanyam R

更新日期：2016-09-01 00:00:00

abstract：:Nanoporous iron oxide (Fe3O4) nanoparticles (NIONPs) have been widely used as promising agents in biomedical applications. Herein, the NIONPs were synthesized by one-step hydrothermal method and well-characterized by FESEM and TEM investigations. Afterwards, their interaction with human serum albumin (HSA) was studied...

journal_title：Journal of biomolecular structure & dynamics

authors： Mehrabi M,Ghasemi MF,Rasti B,Falahati M,Mirzaie A,Hasan A

更新日期：2020-04-15 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：:A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on...

journal_title：Journal of biomolecular structure & dynamics

authors： Grigoriev IV,Rakhmaninova AB,Mironov AA

更新日期：1998-08-01 00:00:00

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：: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：:The hexachlorocyclotriphosphaze compound (N3P3Cl6, HCCP) was reacted with excess (E)-(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-ones (2-11) to produce hexakis[(1-(4-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes (CP 2-11). The structures of products (CP 2-11) were confirmed using eleme...

journal_title：Journal of biomolecular structure & dynamics

authors： Doğan H,Bahar MR,Çalışkan E,Tekin S,Uslu H,Akman F,Koran K,Sandal S,Görgülü AO

更新日期：2020-11-19 00:00:00

abstract：:Melanoma is a malignant cancer of the skin associated with a high mortality. Early medical diagnosis and surgical intervention are essential for the treatment of melanoma. The use of plant-based compounds is an important strategy for the prevention and treatment of different types of cancers. Curcumin is a promising n...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghazaeian M,Khorsandi K,Hosseinzadeh R,Naderi A,Abrahamse H

更新日期：2020-08-07 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 novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mech...

journal_title：Journal of biomolecular structure & dynamics

authors： Tian H,Tao P

更新日期：2020-08-04 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：:In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...

journal_title：Journal of biomolecular structure & dynamics

authors： Sepehri N,Mohammadi-Khanaposhtani M,Asemanipoor N,Hosseini S,Biglar M,Larijani B,Mahdavi M,Hamedifar H,Taslimi P,Sadeghian N,Norizadehtazehkand M,Gulcin I

更新日期：2020-11-23 00:00:00

abstract：:Histone acetyltransferases (HATs) is one among the conspicuous posttranslational modification in eukaryotic cells. p300/CBP Associated Factor (PCAF) and CREB-binding protein (CBP) are the two highly homologous HAT family which are vastly implicated in several diseases like cancer, diabetes, etc. Pentadecylidenemalonat...

journal_title：Journal of biomolecular structure & dynamics

authors： Suryanarayanan V,Singh SK

更新日期：2019-06-01 00:00:00

abstract：:Complexes of NaDNA with the bipyridyl-(ethylenediamine)platintum(II) (abbreviated [(bipy)Pt(en)]2+) molecular ion have been studied in solution via ultraviolet absorption experiments at 260 nm between 50 and 90 degrees C. These measurements, performed as a function of the molar ratio of the [(bipy)Pt(en)]2+ complex to...

journal_title：Journal of biomolecular structure & dynamics

authors： Szabó S,Lee SA

更新日期：2008-08-01 00:00:00

abstract：:The infrared absorption and 1H nuclear magnetic resonance analyses of chloroform solutions of the terminally-blocked segment corresponding to the 2-9 sequence of emerimicins III and IV, -(Aib)3-L-Val-Gly-L-Leu-(Aib)2-, are consistent with the presence of a 3(10)-helical structure of high thermal stability. The crystal...

journal_title：Journal of biomolecular structure & dynamics

authors： Toniolo C,Bonora GM,Bavoso A,Benedetti E,di Blasio B,Pavone V,Pedone C

更新日期：1985-12-01 00:00:00

abstract：:SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodoc...

journal_title：Journal of biomolecular structure & dynamics

authors： Rajendran M,Roy S,Ravichandran K,Mishra B,Gupta DK,Nagarajan S,Arul Selvaraj RC,Provaznik I

更新日期：2020-11-17 00:00:00

abstract：:Inside a living cell there can be a variety of interactions for any given protein, which serve to regulate denaturation and renaturation processes. Insights into some of them can be obtained by in vitro studies using various denaturing agents. In this study, all-atom MD simulations in explicit solvent and NMR relaxati...

journal_title：Journal of biomolecular structure & dynamics

authors： Borkar A,Rout MK,Hosur RV

更新日期：2012-01-01 00:00:00

abstract：:Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have n...

journal_title：Journal of biomolecular structure & dynamics

authors： Elmezayen AD,Yelekçi K

更新日期：2020-07-27 00:00:00

abstract：:Colchicine, a tricyclic alkaloid, has a remarkable range of biological activities. It binds with tubulin and prevents the formation of microtubules. This compound consists of a six membered aromatic ring (A ring), a seven membered troponoid ring (C ring) and another seven membered aliphatic ring (B ring). Using molecu...

journal_title：Journal of biomolecular structure & dynamics

authors： Bothra AK,Roy S,Bhattacharyya B,Mukhopadhyay C

更新日期：1998-04-01 00:00:00

abstract：:Molecular modeling studies have been carried out to investigate the interactions between substrate sialyloligosaccharide (SOS) fragments bearing different glycosidic linkages and influenza virus N9 neuraminidase, a surface glycoprotein of influenza virus subtype N9. The studies revealed that the allowed orientation fo...

journal_title：Journal of biomolecular structure & dynamics

authors： Veluraja K,Suresh MX,Christlet TH,Rafi ZA

更新日期：2001-08-01 00:00:00

abstract：:A potential anti-Human Immunodeficiency Virus (HIV) agent with novel mode of action is urgently needed to fight against drug resistance HIV. The HIV capsid protein is important for both late and early stages of the viral replication cycle and emerged as a promising target for the developing of small molecule inhibitor...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhole RP,Bonde CG,Bonde SC,Chikhale RV,Wavhale RD

更新日期：2021-02-01 00:00:00

abstract：:Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both th...

journal_title：Journal of biomolecular structure & dynamics

authors： Bracht F,de Alencastro RB

更新日期：2016-01-01 00:00:00

abstract：:The reaction mechanisms of two isomeric bay-region diol epoxides of 5-methylchrysene (trans-1,2-dihydroxy-anti-3,4-epoxy-1,2,3,4-tetrahydro-5-methylchrysene (DE-I) and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-5-methylchrysene (DE-II) with double-stranded DNA in aqueous solutions were studied utilizing k...

journal_title：Journal of biomolecular structure & dynamics

authors： Kim MH,Roche CJ,Geacintov NE,Pope M,Pataki J,Harvey RG

更新日期：1986-04-01 00:00:00