当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS期刊下所有文献 > Structural characterization of vivapain-2 and vivapain-3, cysteine proteases from Plasmodium vivax: comparative protein modeling and docking studies.

Structural characterization of vivapain-2 and vivapain-3, cysteine proteases from Plasmodium vivax: comparative protein modeling and docking studies.

Abstract：

:Malaria remains one of the most important infectious diseases in the world. Plasmodial cysteine proteases are proposed to be promising targets for novel antimalarial drug design. Vivapain-2 and vivapain-3 are cysteine proteases from Plasmodium vivax and apparent orthologs of falcipain-2 and falcipain-3 from Plasmodium falciparum. Model structures of vivapain-2 and vivapain-3 have been derived using the comparative protein modeling approach and validated by various structure/geometry verification tools. Correlation between the interaction energies calculated based on the docking studies of the inhibitors and the corresponding association constants (k(ass)) provide additional validation for the structures. Moreover, some of the biochemical differences observed between the vivapains may be explained by the results of the docking studies. The overall structures of the two vivapains are similar to each other as well as to the falcipains with most of the catalytic residues conserved. At the same time, some important differences are observed between the sizes of the binding pockets as well as some of the residues involved in binding. The study suggests a likelihood of developing common inhibitors for these enzymes provided the interesting differences in the binding pockets of these enzymes are critically considered during such an attempt. The results of the current study can be utilized in de novo drug design for effective treatment of malaria.

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Desai PV,Avery MA

doi

10.1080/07391102.2004.10506968

subject

Has Abstract

pub_date

2004-06-01 00:00:00

pages

781-90

issue

6

eissn

0739-1102

issn

1538-0254

pii

d=3016&c=4151&p=12313&do=detail

journal_volume

21

pub_type

杂志文章

相关文献

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS文献大全
  • New wrinkles on polynucleotide duplexes.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.1983.10507453

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

    更新日期：1983-10-01 00:00:00

  • Application of molecular dynamics simulations to spin-labeled oligonucleotides.

    abstract：:The EPR study of spin labeled macromolecules has provided insight into structural and dynamical properties of DNA, proteins, and related systems. While spin labeling has been useful, it is experimentally difficult to determine if the spin label significantly alters the conformation of the macromolecule to which it is ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2005.10507028

    authors： Darian E,Gannett PM

    更新日期：2005-04-01 00:00:00

  • Dissecting water binding sites at protein-protein interfaces: a lesson from the atomic structures in the Protein Data Bank.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1453379

    authors： Mukherjee S,Nithin C,Divakaruni Y,Bahadur RP

    更新日期：2019-03-01 00:00:00

  • Homology modeling, virtual screening and dynamics study of proteins involved in Pebrine - Serine protease inhibitor 106 and spore wall protein 26.

    abstract：:Pebrine is a microsporidian disease caused by Nosema bombycis in Bombyx mori (silk worm) which results in brown/black spots. The affected larvae either spin cocoons which are flimsy with low silk content or not spin a cocoon. It has been hypothesised that Serine Protease Inhibitor 106 (SPN106) is responsible for evasi...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1696704

    authors： U M S,Karunakar P,Krishnamurthy V

    更新日期：2020-10-01 00:00:00

  • Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1095116

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

    更新日期：2016-09-01 00:00:00

  • Effect of seven Indian plant extracts on Fenton reaction-mediated damage to DNA constituents.

    abstract：:The influences of substoichiometric amounts of seven plant extracts in the Fenton reaction-mediated damage to deoxynucleosides, deoxynucleoside monophosphates, deoxynucleoside triphosphates, and supercoiled plasmid DNA were studied to rationalize anticancer properties reported in some of these extracts. Extracts from ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1244493

    authors： Kar I,Chattopadhyaya R

    更新日期：2017-11-01 00:00:00

  • Dynamic instability responses of the substructure living biological cells in the cytoplasm environment using stress-strain size-dependent theory.

    abstract：:Over the last few years, some novel researches in the field of medical science made a tendency to have a therapy without any complications or side-effects of the disease with the aid of prognosis about the behaviors of the substructure living biological cell. Regarding this issue, nonlinear frequency characteristics o...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1751297

    authors： Najaafi N,Jamali M,Habibi M,Sadeghi S,Jung DW,Nabipour N

    更新日期：2020-04-17 00:00:00

  • Structure-based methoxyflavone derivatives with potent inhibitory activity against various influenza neuraminidases.

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

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2019.1680436

    authors： Zang Y,Hao D,Wang H,Yang Z,Liu H,Zhang S

    更新日期：2020-09-01 00:00:00

  • Docking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase.

    abstract：:Simple molecular docking calculations on quercetin, kojic acid and diethylcarbamatodithoic acid using the software package MOE are shown to be close to the geometries reported in the X-ray crystal structures of the protein co-crystallized with the respective ligands. Furthermore, DFT optimization of the docked conform...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1123190

    authors： Malkhasian AY,Howlin BJ

    更新日期：2016-11-01 00:00:00

  • Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1751295

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

    更新日期：2020-05-05 00:00:00

  • A novel method to analyze the similarity of biological sequences.

    abstract：:In this paper, we propose a new method based on the 2-D graphical representation to analyze the similarity of biological sequences and classify the protein secondary structure sequences. Instead of computing some characteristics from the distance matrix, the average area surrounded by the curve and X axis is computed ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2009.10507275

    authors： Huang W,Guo Y,Zhang J

    更新日期：2009-04-01 00:00:00

  • The interaction of beta-lactoglobulin with ciprofloxacin and kanamycin; a spectroscopic and molecular modeling approach.

    abstract：:A vast research has been conducted to find suitable and safe carriers for vital and pH-sensitive drugs including antibiotics. This article reports the use of easily accessible and abundant purified beta-lactoglobulin (β-LG) protein as the potential carrier of widely used Kanamycin (Kana) and Ciprofloxacin (Cip) antibi...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1203819

    authors： Mehraban MH,Odooli S,Yousefi R,Roghanian R,Motovali-Bashi M,Moosavi-Movahedi AA,Ghasemi Y

    更新日期：2017-07-01 00:00:00

  • Critical effects on binding of epidermal growth factor produced by amino acid substitutions.

    abstract：:Epidermal growth factor (EGF) plays important roles in multiple biological processes, such as the regulation of cell growth, proliferation, and differentiation. EGF exerts their pharmacologic effects via receptor-mediated mechanism associated with high affinity to epidermal growth factor receptor (EGFR) on the cell su...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1171799

    authors： Mehrabi M,Khodarahmi R,Shahlaei M

    更新日期：2017-04-01 00:00:00

  • The size of the topological domain modulates the B-Z transition of a (TG)n containing repeat.

    abstract：:Under negative superhelical stress, long (TG)n containing repeats experience a stepwise multiple B-Z transitions. We have investigated the effect of the plasmid size on this transitional behavior. A 66-bp (TG)n containing repeat from the 5'-untranscribed region of mouse ribosomal DNA was inserted in a 3-kb, a 6.5-kb a...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1995.10508820

    authors： Albert AC,Leng M,Rahmouni AR

    更新日期：1995-08-01 00:00:00

  • Probing site-specific interactions in protein-DNA complexes using heteronuclear NMR spectroscopy and molecular modeling: binding of Cro repressor to OR3.

    abstract：:In this paper, a general method is developed to study site-specific interactions in DNA-protein complexes using heteronuclear NMR spectroscopy and molecular modeling. This method involves two steps: (a) homonuclear 1H NMR and molecular modeling are used to develop a low resolution model and (b) 15N7-guanosine containi...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1998.10508222

    authors： Edwards CA,Tung CS,Silks LA,Gatewood JM,Fee JA,Mariappan SV

    更新日期：1998-08-01 00:00:00

  • Amino acid/water interactions study: a new amino acid scale.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2013.800994

    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

  • 1,2,3-Triazole substituted phthalocyanine metal complexes as potential inhibitors for anticholinesterase and antidiabetic enzymes with molecular docking studies.

    abstract：:In recent years, acetylcholinesterase (AChE) and α-glycosidase (α-gly) inhibition have emerged as a promising and important approach for pharmacological intervention in many diseases such as glaucoma, epilepsy, obesity, cancer, and Alzheimer's. In this manner, the preparation and enzyme inhibition activities of periph...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1857842

    authors： Koçyiğit ÜM,Taslimi P,Tüzün B,Yakan H,Muğlu H,Güzel E

    更新日期：2020-12-09 00:00:00

  • Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances.

    abstract：:Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1998.10508209

    authors： Shchelkanov MYu,Starikov NS,Yaroslavtsev IV,Tsvetkov PO,Yudin AN,Denisov MV,Slavsky AA,Vedenov AA,Karamov EV

    更新日期：1998-04-01 00:00:00

  • Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

    abstract：:Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buc...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2005.10507018

    authors： Danilov VI,Anisimov VM

    更新日期：2005-02-01 00:00:00

  • Inactivation kinetics of beta-N-acetyl-D-glucosaminidase from green crab (Scylla serrata) in dioxane solution.

    abstract：:Beta-N-acetyl-D-glucosaminidase (NAGase, EC.3.2.1.52), which catalyzes the cleavage of N-acetylglucosamine polymers, is a composition of chitinase and cooperates with endo-chitinase and exo-chitinase to disintegrate chitin into N-acetylglucosamine (NAG). In this investigation, A NAGase from green crab (Scylla serrata)...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2009.10507266

    authors： Xie JJ,Chen CQ,Yan YW,Zhang JP,Lin JC,Wang Q,Zhou HT,Chen QX

    更新日期：2009-02-01 00:00:00

  • The terminal phosphate in d(pGpG) reduces self-association.

    abstract：:An investigation of the self-association behavior of 2'-deoxy[5'-phosphate-guanylyl-(3'-5')-guanosine] (d(pGpG)) in the presence of Na+ and K+ ions has been carried out by 1H and 31P NMR and FTIR spectroscopy. A comparison has been made of the self- association behavior of d(pGpG) with that of the related dinucleotide...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1999.10508386

    authors： Kawasaki MM,Walmsley JA

    更新日期：1999-12-01 00:00:00

  • How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1046936

    authors： Brovarets' OO,Hovorun DM

    更新日期：2015-01-01 00:00:00

  • Study on the binding characteristics of hydroxylated polybrominated diphenyl ethers and thyroid transporters using the multispectral technique and computational simulation.

    abstract：:Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1461134

    authors： Wei Y,Yi Z,Xu J,Yang W,Yang L,Liu H

    更新日期：2019-04-01 00:00:00

  • Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2014.948070

    authors： Mamidi AS,Surolia A

    更新日期：2015-01-01 00:00:00

  • Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase.

    abstract：:Catalase is an important antioxidant enzyme that catalyzes the disproportionation of H2O2 into harmless water and molecular oxygen. Due to various applications of the enzyme in different sectors of industry as well as medicine, the enhancement of stability of the enzyme is important. Effect of various classes of compa...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2012.742460

    authors： Sepasi Tehrani H,Moosavi-Movahedi AA,Ghourchian H,Ahmad F,Kiany A,Atri MS,Ariaeenejad Sh,Kavousi K,Saboury AA

    更新日期：2013-12-01 00:00:00

  • Genetic and biochemical manipulations of the small ribosomal subunit from Thermus thermophilus HB8.

    abstract：:Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains reg...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2000.10506553

    authors： Auerbach T,Pioletti M,Avila H,Anagnostopoulos K,Weinstein S,Franceschi F,Yonath A

    更新日期：2000-02-01 00:00:00

  • The four repeat Giardia lamblia telomere forms tetramolecular G-quadruplex with antiparallel topology.

    abstract：:Guanine rich DNA sequences of regulatory genomic regions form secondary structures known as G-quadruplexes usually stabilized by tetrads of Hoogsteen hydrogen bonded guanines. The in vivo existence of G-quadruplexes ascertains their biological roles. Human telomeric repeats are the most studied G-rich sequences. The f...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1623074

    authors： Bansal A,Kukreti S

    更新日期：2020-04-01 00:00:00

  • Peculiarities of interaction of porphyrins with tRNA at low ionic strength.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2010.10507348

    authors： Dalyan Y,Vardanyan I,Chavushyan A,Balayan G

    更新日期：2010-08-01 00:00:00

  • Spectroscopic and molecular modeling approaches to investigate the binding of proton pump inhibitors to human serum albumin.

    abstract：:The interaction between two proton pump inhibitors viz., omeprazole (OME) and esomeprazole (EPZ) with human serum albumin (HSA) was studied by fluorescence, absorption, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), voltammetry, and molecular modeling approaches. The Stern-Volmer quenching c...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1251337

    authors： Pawar SK,Punith R,Naik RS,Seetharamappa J

    更新日期：2017-11-01 00:00:00

  • Docking analysis insights quercetin can be a non-antibiotic adjuvant by inhibiting Mmr drug efflux pump in Mycobacterium sp. and its homologue EmrE in Escherichia coli.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2014.974211

    authors： Suriyanarayanan B,Sarojini Santhosh R

    更新日期：2015-01-01 00:00:00