Modeling of Neuropeptide Receptors Y1, Y4, Y5, and Docking Studies with Neuropeptide Antagonist Analogues: Implications for Selectivity.

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 binding site identification is an important step in developing new therapeutic agents. We have attempted to model the three NPY receptor types, Y1, Y4, and Y5 using homology modeling and threading methods. The models are consistent with previously reported experimental evidence. To understand the interaction and selectivity of NPY analogues with different neuropeptide receptors, docking studies of two neuropeptide analogues (BVD10 and BVD15) with receptors Y1 and Y4 were carried out. Results of the docking studies indicated that the interaction of ligands BVD10 and BVD15 with Y1 and Y4 receptors are different. These results were evaluated for selectivity of peptide analogues BVD10 and BVD15 towards the receptors.

journal_name

J Biomol Struct Dyn

authors

Jois SD,Nagarajarao LM,Prabhakaran M,Balasubramaniam A

doi

10.1080/07391102.2004.10506987

subject

Has Abstract

pub_date

2004-08-01 00:00:00

pages

497-508

issue

1

eissn

0739-1102

issn

1538-0254

journal_volume

22

pub_type

杂志文章
  • Long, chiral polypeptide 3(10)-helices at atomic resolution.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.1988.10506428

    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

  • Possible involvement of coaxially stacked double pseudoknots in the regulation of -1 programmed ribosomal frameshifting in RNA viruses.

    abstract::-1 programmed ribosomal frameshifting (PRF) in viruses is often stimulated by a pseudoknot downstream from the slippery sequence. At the PRF junction of HIV-1, transmissible gastroenteritis virus (TGEV), Barmah Forest virus (BFV), Fort Morgan virus (FMV), and Equine arteritis virus (EAV), we identified potential doubl...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2014.956149

    authors: Wang G,Yang Y,Huang X,Du Z

    更新日期:2015-01-01 00:00:00

  • Characteristics, dynamics and mechanisms of actions of some major stress-induced biomacromolecules; addressing Artemia as an excellent biological model.

    abstract::Stress tolerance is one of the most prominent and interesting topics in biology since many macro- and micro-adaptations have evolved in resistant organisms that are worth studying. When it comes to confronting various environmental stressors, the extremophile Artemia is unrivaled in the animal kingdom. In the present ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1796793

    authors: Khodajou-Masouleh H,Shahangian SS,Attar F,H Sajedi R,Rasti B

    更新日期:2020-07-31 00:00:00

  • A new bithiazole derivative with intercalative properties.

    abstract::In the course of studies related to new molecules with intercalative properties, we have been led to design and synthesize a bithiazole derivative, namely the 2-phenyl-6-[2'-(4'-(ethoxy-carbonyl)thiazolyl)]thiazolo[3,2- b][1,2,4]triazole (PETT). Its interaction with calf thymus DNA was studied using thermal denaturati...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1986.10506341

    authors: Houssin R,Helbecque N,Bernier JL,Henichart JP

    更新日期:1986-10-01 00:00:00

  • Human microtubule affinity-regulating kinase 4 is stable at extremes of pH.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1074942

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

    更新日期:2016-06-01 00:00:00

  • NMR and molecular dynamics studies of tachykinins: conformation of substance P fragment 4-11.

    abstract::The conformation of the C-terminal octapeptide fragment of Substance P (SP4-11, Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2) has been investigated by 2D-NMR and MD methods. The octapeptide exists in a blend of conformations. The molecule seems to shuttle between conformations with gamma-bends either at Phe5 or Gly6 or Gln3 or...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508286

    authors: Coutinho E,Kamath S,Saran A,Srivastava S

    更新日期:1998-12-01 00:00:00

  • Virtual screening, docking, and dynamics of potential new inhibitors of dihydrofolate reductase from Yersinia pestis.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1110832

    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

  • Bioinformatics exploration of PAK1 (P21-activated kinase-1) revealed potential network gene elements in breast invasive carcinoma.

    abstract::P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore it...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1216894

    authors: Yellapu NK,Pulaganti M,Pakala SB

    更新日期:2017-08-01 00:00:00

  • Metal binding and conformational studies of the calcium binding domain of NADPH oxidase 5 reveal its similarity and difference to calmodulin.

    abstract::The superoxide-generating activity of Nox5 is regulated by Ca2+ flux, primarily through its self-contained calcium binding domain (EFD). Upon Ca2+ binding, Nox5's EFD undergoes a conformational change that exposes its buried hydrophobic residues. Previously, we determined the Ca2+ binding constants of the N-terminal h...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1633409

    authors: Wei CC,Fabry E,Hay E,Lloyd L,Kaufman N,Yang YP,Stuehr DJ

    更新日期:2020-05-01 00:00:00

  • Conformation of DNA-DNA polymerase I complex observed by scanning tunneling microscopy.

    abstract::The conformation of a complex of a 41 mer/31 mer DNA fragment and the Klenow fragment of DNA polymerase I of Escherichia coli was studied by scanning tunnelling microscopy (STM). The results shows that near two turns of double helix of this DNA fragment was outside of enzyme while another part containing more than one...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1991.10507909

    authors: Lu CD,Li MQ,Qui MY,Yao XW,Xu YL,Gu MM,Hu J

    更新日期:1991-10-01 00:00:00

  • Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508761

    authors: Seshadri K,Rao VS,Vishveshwara S

    更新日期:1994-12-01 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

  • Hairpin induced slippage and hyper-methylation of the fragile X DNA triplets.

    abstract::The fragile X triplet repeats, (GCC)n x (GGC)n are located at the 5' untranslated region of the FMR-1 gene. Inordinate repeat expansion and hyper-methylation of the CpG islands inside the repeat lead to the suppression of the FMR-1 gene and the subsequent onset and progression of the disease. Previously, we have shown...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508989

    authors: Chen X,Mariappan SV,Moyzis RK,Bradbury EM,Gupta G

    更新日期:1998-02-01 00:00:00

  • Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection.

    abstract::Mycobacterium tuberculosis (Mtb), the pathogen of tuberculosis (TB), is one of the most infectious bacteria in the world. The traditional strategy to combat TB involves targeting the pathogen directly; however, the rapid evolution of drug resistance lessens the efficiency of this anti-TB method. Therefore, in recent y...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2016.1157037

    authors: Quan Y,Xiong L,Chen J,Zhang HY

    更新日期:2017-02-01 00:00:00

  • Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

    abstract::The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of comple...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1326320

    authors: Shamsi A,Ahmed A,Bano B

    更新日期:2018-05-01 00:00:00

  • Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex.

    abstract::MutSα is the most abundant mismatch-binding factor of human DNA mismatch repair (MMR) proteins. MMR maintains genetic stability by recognizing and repairing DNA defects. Failure to accomplish their function may lead to cancer. In addition, MutSα recognizes at least some types of DNA damage making it a target for antic...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2013.799437

    authors: Negureanu L,Salsbury FR Jr

    更新日期:2014-01-01 00:00:00

  • Molecular dynamics simulation of colchicinoids.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508219

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

    更新日期:1998-04-01 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

  • Unique hole-trapping property of the human telomere sequence.

    abstract::The hypothetical protection of genes from oxidative damage provided by the G-rich telomeric overhangs located at the end of chromosomes, which consist, in humans, of single strands of TTAGGG sequence repeats, is investigated here. First principle Moller-Plesset perturbation theory calculations reveal that the TTAGGG h...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2011.10507405

    authors: Cauët E

    更新日期:2011-12-01 00:00:00

  • Nucleosome positioning by sequence, state of the art and apparent finale.

    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

    pub_type: 杂志文章

    doi:10.1080/073911010010524944

    authors: Trifonov EN

    更新日期:2010-06-01 00:00:00

  • An insight to the dynamics of conserved water molecular triad in IMPDH II (human): recognition of cofactor and substrate to catalytic Arg 322.

    abstract::Inosine 5' monophosphate dehydrogenase (IMPDH II) is a key enzyme involved in the de novo biosynthesis pathway of purine nucleotides and is also considered to be an excellent target for cancer inhibitor design. The conserve R 322 residue (in human) is thought to play some role in the recognition of inhibitor and cofac...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507304

    authors: Bairagya HR,Mukhopadhyay BP,Sekar K

    更新日期:2009-10-01 00:00:00

  • An ultraviolet melting study of the stability of the DNA double helix in the NaDNA-bipyridyl-(ethylenediamine)platintum(II) complex.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507227

    authors: Szabó S,Lee SA

    更新日期:2008-08-01 00:00:00

  • Comparison of complex DNA mixtures with generic oligonucleotide microchips.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2001.10506709

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

    更新日期:2001-06-01 00:00:00

  • Structure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1758787

    authors: Shukla R,Shukla H,Tripathi T

    更新日期:2020-04-30 00:00:00

  • New insight into the molecular mechanism of the trehalose effect on urate oxidase stability.

    abstract::Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinan...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1828167

    authors: Taherimehr Z,Zaboli M,Torkzadeh-Mahani M

    更新日期:2020-10-01 00:00:00

  • An NMR study of the polymorphous behavior of the mismatched DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. The B, Z, and hairpin forms.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.1987.10507691

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

    更新日期:1987-06-01 00:00:00

  • Probing the effect of a plus 1bp frameshift mutation in protein-DNA interface of domestication gene, NAMB1, in wheat.

    abstract::Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1680435

    authors: Kaul T,Eswaran M,Ahmad S,Thangaraj A,Jain R,Kaul R,Raman NM,Bharti J

    更新日期:2020-08-01 00:00:00

  • Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial.

    abstract::Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded c...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1848629

    authors: Mishra M,Singh V,Tellis MB,Joshi RS,Pandey KC,Singh S

    更新日期:2020-12-09 00:00:00

  • Single-stranded DNA and RNA targeted triplex-formation: UV, CD and molecular modeling studies of foldback triplexes containing different RNA, 2'-OMe-RNA and DNA strand combinations.

    abstract::We studied the influence of different 2'-OMe-RNA and DNA strand combinations on single strand targeted foldback triplex formation in the Py.Pu:Py motif using ultraviolet (UV) and circular dichroism (CD) spectroscopy, and molecular modeling. The study of eight combinations of triplexes (D.D:D, R*.D:D, D.D:R*, R*.D:R*, ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1997.10508174

    authors: Kandimalla ER,Venkataraman G,Sasisekharan V,Agrawal S

    更新日期:1997-06-01 00:00:00

  • Molecular modeling study of the norfloxacin-DNA complex.

    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

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506811

    authors: Lee HM,Kim JK,Kim SK

    更新日期:2002-06-01 00:00:00