abstract：:In the present work, we propose to design drugs that target the enzyme dihydrofolate redutase (DHFR) as a means of a novel drug therapy against plague. Potential inhibitors of DHFR from Yersinia pestis (YpDHFR) were selected by virtual screening and subjected to docking, molecular dynamics (MD) simulations, and Poisso...

journal_title：Journal of biomolecular structure & dynamics

authors： Bastos Lda C,de Souza FR,Guimarães AP,Sirouspour M,Cuya Guizado TR,Forgione P,Ramalho TC,França TC

更新日期：2016-10-01 00:00:00

abstract：:The present study employed the spectroscopic techniques, i.e. fluorescence, and circular dichroism (CD) and the molecular docking approach to investigate the mechanism of interaction of a potent anticancer glucosinolate, sinigrin (SIN), with bovine serum albumin (BSA). SIN binding to BSA resulted in the quenching of i...

journal_title：Journal of biomolecular structure & dynamics

authors： Awasthi S,Saraswathi NT

更新日期：2016-10-01 00:00:00

abstract：:The Transformer2 (Tra2) proteins in humans are homologues of the Drosophila Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Ghosh P,Grellscheid SN,Sowdhamini R

更新日期：2016-09-01 00:00:00

abstract：:With the explosive growth of protein sequences entering into protein data banks in the post-genomic era, it is highly demanded to develop automated methods for rapidly and effectively identifying the protein-protein binding sites (PPBSs) based on the sequence information alone. To address this problem, we proposed a p...

journal_title：Journal of biomolecular structure & dynamics

authors： Jia J,Liu Z,Xiao X,Liu B,Chou KC

更新日期：2016-09-01 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：: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：:For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in ...

journal_title：Journal of biomolecular structure & dynamics

authors： Rosandić M,Vlahović I,Glunčić M,Paar V

更新日期：2016-07-01 00:00:00

abstract：:Protein kinase C (PKC) isozymes are important regulatory enzymes that have been implicated in many diseases, including cancer, Alzheimer's disease, and in the eradication of HIV/AIDS. Given their potential clinical ramifications, PKC modulators, e.g. phorbol esters and bryostatin, are also of great interest in the dru...

journal_title：Journal of biomolecular structure & dynamics

authors： Thangsunan P,Tateing S,Hannongbua S,Suree N

更新日期：2016-07-01 00:00:00

abstract：:About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...

journal_title：Journal of biomolecular structure & dynamics

authors： Gogoi P,Chandravanshi M,Mandal SK,Srivastava A,Kanaujia SP

更新日期：2016-07-01 00:00:00

abstract：:Aggregation of amyloid peptide (Aβ) has been shown to be directly related to progression of Alzheimer's disease (AD). Aβ is neurotoxic and its deposition and aggregation ultimately lead to cell death. In our previous work, we reported flavonoid derivative (compound 1) showing promising result in transgenic AD model of...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumar A,Srivastava S,Tripathi S,Singh SK,Srikrishna S,Sharma A

更新日期：2016-06-01 00:00:00

abstract：:MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-ter...

journal_title：Journal of biomolecular structure & dynamics

authors： Naz F,Singh P,Islam A,Ahmad F,Imtaiyaz Hassan M

更新日期：2016-06-01 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：:Trichoderma spp. are well-known bioagents for the plant growth promotion and pathogen suppression. The beneficial activities of the fungus Trichoderma spp. are attributed to their ability to produce and secrete certain secondary metabolites such as trichodermin that belongs to trichothecene family of molecules. The in...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumari I,Chaudhary N,Sandhu P,Ahmed M,Akhter Y

更新日期：2016-06-01 00:00:00

abstract：:Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked whic...

journal_title：Journal of biomolecular structure & dynamics

authors： Kumalo HM,Bhakat S,Soliman ME

更新日期：2016-05-01 00:00:00

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：: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：:Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural t...

journal_title：Journal of biomolecular structure & dynamics

authors： Abhinand PA,Shaikh F,Bhakat S,Radadiya A,Bhaskar LV,Shah A,Ragunath PK

更新日期：2016-01-01 00:00:00

abstract：:The nucleoprotein (NP) binds the viral RNA genome as oligomers assembled with the polymerase in a ribonucleoprotein complex required for transcription and replication of influenza A virus. Novel antiviral candidates targeting the nucleoprotein either induced higher order oligomers or reduced NP oligomerization by targ...

journal_title：Journal of biomolecular structure & dynamics

authors： Tarus B,Bertrand H,Zedda G,Di Primo C,Quideau S,Slama-Schwok A

更新日期：2015-09-01 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：:Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...

journal_title：Journal of biomolecular structure & dynamics

authors： Jamshidi S,Jalili S,Rafii-Tabar H

更新日期：2015-01-01 00:00:00

abstract：:Based on the known structural model for reverse transcription initiation complex of the human immunodeficiency virus type 1 (HIV-1) MAL isolate, we attempted to predict a structural behavior of MAL-like templates (CRF01_AE, subtype G and CRF02_AG) within the initiation complex by in silico experiments. Switches from t...

journal_title：Journal of biomolecular structure & dynamics

authors： Kolomiets IN,Zarudnaya MI,Potyahaylo AL,Hovorun DM

更新日期：2015-01-01 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：:In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pat...

journal_title：Journal of biomolecular structure & dynamics

authors： Brovarets' OO,Hovorun DM

更新日期：2015-01-01 00:00:00

abstract：:Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malar...

journal_title：Journal of biomolecular structure & dynamics

authors： Omotuyi IO,Hamada T

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：:Earlier identified strongest nucleosome DNA sequences of A. thaliana, those with visible 10-11 base sequence periodicity, are mapped along chromosomes. Resulting positional distributions reveal distinct maxima, one per chromosome, located in the centromere regions. Sequence-directed nucleosome mapping demonstrates tha...

journal_title：Journal of biomolecular structure & dynamics

authors： Salih B,Trifonov EN

更新日期：2015-01-01 00:00:00

abstract：:Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and...

journal_title：Journal of biomolecular structure & dynamics

authors： Tanneeru K,Balla AR,Guruprasad L

更新日期：2015-01-01 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：:Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs co...

journal_title：Journal of biomolecular structure & dynamics

authors： Mani A,Gupta DK

更新日期：2015-01-01 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：:The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Ebrahimi M,Khayamian T,Hadadzadeh H,Sayed Tabatabaei BE,Jannesari Z,Khaksar G

更新日期：2015-01-01 00:00:00

abstract：:α-helices are the most common form of secondary structure found in proteins. In order to study controlled protein folding, as well as manipulate the interface of helical peptides with targets in protein-protein interactions, many techniques have been developed to induce and stabilize α-helical structure in short synth...

journal_title：Journal of biomolecular structure & dynamics

authors： Guarracino DA,Alabanza AM,Robertson CT,Sanghvi SS

更新日期：2015-01-01 00:00:00

abstract：:Peptide- and protein-protein dockings were carried out on β2-adrenergic receptor (β2AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two β2AR monomers, thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially, a porti...

journal_title：Journal of biomolecular structure & dynamics

authors： Koroglu A,Akten ED

更新日期：2015-01-01 00:00:00

abstract：:Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) sim...

journal_title：Journal of biomolecular structure & dynamics

authors： Song W,Guo JT

更新日期：2015-01-01 00:00:00

abstract：:During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promo...

journal_title：Journal of biomolecular structure & dynamics

authors： Mitra S,Das P,Samadder A,Das S,Betai R,Chakrabarti J

更新日期：2015-01-01 00:00:00

abstract：:A conceptually new idea in quantitative structure-activity relationships (QSAR) which makes use of ensembles from molecular dynamics (MD) trajectories and information retrieved from enzyme-inhibitor binding thermodynamics is presented in this study. This new methodology, termed ensemble comparative residue interaction...

journal_title：Journal of biomolecular structure & dynamics

authors： Khedkar VM,Joseph J,Pissurlenkar R,Saran A,Coutinho EC

更新日期：2015-01-01 00:00:00

abstract：:Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-gly...

journal_title：Journal of biomolecular structure & dynamics

authors： Mamidi AS,Surolia A

更新日期：2015-01-01 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：:Our previous work on structural polymorphism shown at a single nucleotide polymorphism (SNP) (A → G) site located on HS4 region of locus control region (LCR) of β-globin gene has established a hairpin → duplex equilibrium corresponding to A → B like DNA transition (Kaushik M, Kukreti, R., Grover, D., Brahmachari, S.K....

journal_title：Journal of biomolecular structure & dynamics

authors： Kaushik M,Kukreti S

更新日期：2015-01-01 00:00:00

abstract：:Drug efflux pumps (EP) like Mmr in Mycobacterium transported drugs out of cell, a main reason for drug resistance developing in Mycobacterium tuberculosis. In this in silico study, mainly analysed EP inhibitory potential of a plant-derived flavonoid, quercetin, through docking analysis. Mmr present in Mycobacterium sm...

journal_title：Journal of biomolecular structure & dynamics

authors： Suriyanarayanan B,Sarojini Santhosh R

更新日期：2015-01-01 00:00:00