Long, chiral polypeptide 3(10)-helices at atomic resolution.

abstract：:Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluoresc...

journal_title：Journal of biomolecular structure & dynamics

authors： Kandandapani S,Ridzwan NFW,Mohamad SB,Tayyab S

更新日期：2020-09-01 00:00:00

abstract：:The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (H...

journal_title：Journal of biomolecular structure & dynamics

authors： Bischoff G,Bischoff R,Birch-Hirschfeld E,Gromann U,Lindau S,Meister WV,de A Bambirra S,Bohley C,Hoffmann S

更新日期：1998-10-01 00:00:00

abstract：:Preceding experimental findings revealed that the release of indomethacin decreased when a folate conjugate G4-PAMAM (folate-G4-PAMAM) dendrimer was used compared with its unconjugated dendrimer (G4-PAMAM). Further, better encapsulation of the conjugated dendrimer was achieved, information useful for elucidating the s...

journal_title：Journal of biomolecular structure & dynamics

authors： Martínez-Muñoz A,Correa-Basurto J,Bello M

更新日期：2020-12-21 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：: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：:Geometry optimizations and energy calculations have been carried out via molecular orbital methods at the density functional B3LYP/LANL2DZ level on the molecules PO3-, OPO3(3-), HOPO3(2-), CH3OPO3(2-), H(CH3OPO3)-, O(PO3)2(4-), HO(PO3)2(3-), CH2(PO3)2(4-), (CH3OPO2)O(PO3)3-, O(PO3)3(5-), HO(PO3)3(4-), (PO3)3(3-), (CH3...

journal_title：Journal of biomolecular structure & dynamics

authors： Cini R,Chindamo D,Catenaccio M,Lorenzini S,Marcolongo R

更新日期：2000-08-01 00:00:00

abstract：:The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subs...

journal_title：Journal of biomolecular structure & dynamics

authors： de Groot BL,Amadei A,van Aalten DM,Berendsen HJ

更新日期：1996-04-01 00:00:00

abstract：:Protein folding remains an unsolved problem as main-chain, side-chain, and solvent interactions remain entangled and have been hard to resolve. Polyalanines are promising models to analyze protein folding initiation and propagation structurally as well as energetically. In the present work, the effect of chain-length ...

journal_title：Journal of biomolecular structure & dynamics

authors： Goyal B,Kumar A,Srivastava KR,Durani S

更新日期：2017-07-01 00:00:00

abstract：:Chlamydia trachomatis (C.t) is a major causative of infectious blindness in world. It is a real challenge to combat Chlamydial infection as it is an intracellular pathogen. Hence, it is essential to determine the most potential targets of C.t in order to inhibit or suppress its virulence during its infectious phase. T...

journal_title：Journal of biomolecular structure & dynamics

authors： Sadhasivam A,Nagarajan H,Umashankar V

更新日期：2020-07-01 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：: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：:Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degr...

journal_title：Journal of biomolecular structure & dynamics

authors： Singha DL,Maharana J,Panda D,Dehury B,Modi MK,Singh S

更新日期：2020-05-05 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：: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：: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：: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 aim of this study was to attempt to determine the extent to which the chemical shifts of the nonexchangeable base protons of a DNA helix depend upon the base sequence. We measured the proton NMR spectra of twelve decadeoxynucleotides in order to carry out a "statistical" treatment. In the helices, the chemical shi...

journal_title：Journal of biomolecular structure & dynamics

authors： Shindo H,Okhubo S,Matsumoto U,Giessner-Prettre C,Zon G

更新日期：1988-02-01 00:00:00

abstract：:Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residue...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhang T,Faraggi E,Xue B,Dunker AK,Uversky VN,Zhou Y

更新日期：2012-01-01 00:00:00

abstract：:The fluorescent 2-aminopurine probe (2-AP) incorporated into the loop of 23-mer RNA hairpin of HIV-1 genome dimerization initiation site (DIS) was used for discrimination of specific and unspecific binding of paromomycin and spermine to the kissing loop dimer (KD) formed in solution. While both ligands stabilized the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kaluzhny DN,Beniaminov AD,Minyat EE

更新日期：2008-06-01 00:00:00

abstract：:Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

journal_title：Journal of biomolecular structure & dynamics

authors： Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

更新日期：1994-02-01 00:00:00

abstract：:Abstract Neuropeptide Y (NPY), receptors belong to the G-protein coupled receptor superfamily. NPY mediates several physiological responses, such as blood pressure, food intake, sedation. These actions of NPY are mediated by six receptor subtypes denoted as Y(1)-Y(5) and y(6). Modeling of receptor subtypes and bindi...

journal_title：Journal of biomolecular structure & dynamics

authors： Jois SD,Nagarajarao LM,Prabhakaran M,Balasubramaniam A

更新日期：2004-08-01 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：:EhCPADH is a protein complex involved in the virulence of Entamoeba histolytica, the protozoan responsible for human amebiasis. It is formed by the EhCP112 cysteine protease and the EhADH adhesin. To explore the molecular basis of the complex formation, three-dimensional models were built for both proteins and molecul...

journal_title：Journal of biomolecular structure & dynamics

authors： Montaño S,Orozco E,Correa-Basurto J,Bello M,Chávez-Munguía B,Betanzos A

更新日期：2017-02-01 00:00:00

abstract：:Galantamine (Gnt) is a natural alkaloid inhibitor of acetylcholinesterase and is presently one of the most used drugs in the treatment against Alzheimer's disease during both the initial and intermediate stages. Among several natural Gnt derivatives, sanguinine (Sng) and lycoramine (Lyc) attract attention because of t...

journal_title：Journal of biomolecular structure & dynamics

authors： Rocha REO,Lima LHF

更新日期：2019-04-01 00:00:00

abstract：:A general method for generation of base-pairs in a curved DNA structure, for any prescribed values of helical parameters--unit rise (h), unit twist (theta), wedge roll (theta R) and wedge tilt (theta T), propeller twist (theta p) and displacement (D) is described. Its application for generation of uniform as well curv...

journal_title：Journal of biomolecular structure & dynamics

authors： Bhattacharya D,Bansal M

更新日期：1988-08-01 00:00:00

abstract：:The structural and energetical characteristics of the complexes formed between two auto-complementary DNA dodecamers, d(CGCGAATTCGCG)2, and d(GCGCAATTGCGC)2, and two novel netropsin (I) and glycine-netropsin (II) conjugates of a tricationic water-soluble porphyrin are investigated in detail by means of theoretical com...

journal_title：Journal of biomolecular structure & dynamics

authors： Perrée-Fauvet M,Gresh N

更新日期：1994-06-01 00:00:00

abstract：:Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolaskar AS,Joshi RR

更新日期：1998-06-01 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：: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：:Plasma membrane of each micro-organism has a unique set of lipid composition as a consequence of the environmental adaptation or a response to exposure to antimicrobial peptides (AMPs) as antibiotic agents. Understanding the relationship between lipid composition and action of antimicrobial peptides or considering how...

journal_title：Journal of biomolecular structure & dynamics

authors： Rahmanpour A,Ghahremanpour MM,Mehrnejad F,Moghaddam ME

更新日期：2013-12-01 00:00:00