当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS期刊下所有文献 > Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles.

Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles.

Abstract：

:Human major histocompatibility complex class I (MHC I) - or human leukocyte antigen (HLA) - proteins present intracellularly processed peptides to cytotoxic T lymphocytes in the adaptive immune response to pathogens. A high level of polymorphism in human MHC I proteins defines the peptide-binding specificity of thousands of different MHC alleles. However, polymorphism as well as the peptide ligand can also affect the global dynamics of the complex. In this study, we conducted classical molecular dynamics simulations of two HLA alleles, the ankylosing spondylitis (AS) associated/tapasin-dependent HLA-B*27:05 and nondisease-associated/tapasin-independent HLA-B*27:09, both in peptide-free forms as well as complex with four different peptides ligands. Our results indicate that in peptide-free form, the single amino acid substitution distinguishing the two alleles (D116H), leads to a weaker dynamic coupling of residues in the tapasin-dependent HLA-B*27:05. In peptide-bound form, several residues of the binding-groove, mostly in A and B pockets, show hinge-like behavior in the global motion of the MHC. Moreover, allele-dependent changes are shown in residue interactions, affecting the B-pocket as well as the beta-2-microglobulin (β2m)-facing residues of the HLA chain.

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Serçinoğlu O,Ozbek P

doi

10.1080/07391102.2017.1295884

subject

Has Abstract

pub_date

2018-02-01 00:00:00

pages

724-740

issue

3

eissn

0739-1102

issn

1538-0254

journal_volume

36

pub_type

杂志文章

相关文献

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS文献大全
  • The effects of cobalt-hexammine and cobalt-pentammine cations on the solution structure of calf-thymus DNA. DNA condensation and structural features studied by FTIR difference spectroscopy.

    abstract：:The interaction of calf-thymus DNA with cobalt-hexammine and cobalt-pentammine cations was investigated, in aqueous solution at pH 6-7 with cation/DNA(phosphate) molar ratios r = 1/80, 1/40, 1/20, 1/10, 1/4, 1/2 and 1, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between spectral chang...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1993.10508711

    authors： Tajmir-Riahi HA,Naoui M,Ahmad R

    更新日期：1993-08-01 00:00:00

  • Variability analysis of HIV-1 gp120 V3 region: I. Point estimators for the amino acid distribution characteristics.

    abstract：:Enumerating procedure for symbol sequences is proposed. Relationship between Hamming distance for symbol sequences and Euclidean distance for corresponding enumerations is established, and more universal Hamming-transformed Euclidean measure is constructed. A distribution function of amino acid substitutions and some ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1997.10508187

    authors： Shchelkanov MYu,Yudin AN,Antonov AV,Starikov NS,Vedenov AA,Karamov EV

    更新日期：1997-10-01 00:00:00

  • Investigation of flap flexibility of β-secretase using molecular dynamic simulations.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1064831

    authors： Kumalo HM,Bhakat S,Soliman ME

    更新日期：2016-05-01 00:00:00

  • Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation.

    abstract：:Cell-division protein kinases (CDKs) are gorgeous examples of targets for the helpful treatment of cancer by using multi-target inhibitors. Specifically, targeting cell-division protein kinase1/cyclin B (CDK1/Cyclin B), cell-division protein kinase 2/cyclin A (CDK2/Cyclin A) and cell-division protein kinase 4/cyclin D...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1742792

    authors： Al-Khafaji K,Taskin Tok T

    更新日期：2020-03-24 00:00:00

  • Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4' benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations.

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1074943

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

    更新日期：2016-06-01 00:00:00

  • Identify protein-coding genes in the genomes of Aeropyrum pernix K1 and Chlorobium tepidum TLS.

    abstract：:The problem that how many protein-coding genes there are in the genome of Aeropyrum pernix K1 has confused many scientists since the sequencing in 1999. In this paper, the protein-coding genes in A. pernix K1 are identified from the original and current NITE annotation by using the Aper_ORFs method. Consequently, 702 ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2009.10507256

    authors： Guo FB,Lin Y

    更新日期：2009-02-01 00:00:00

  • Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes.

    abstract：:PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 in...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1654410

    authors： Wu J,Sun Y,Zhou H,Ma Y,Wang R

    更新日期：2020-07-01 00:00:00

  • Perturbations in the catecholamine metabolism and protective effect of "3-(3, 4-dimethoxy phenyl)-1-4(methoxy phenyl) prop-2-en-1-one" during ketamine-induced schizophrenia: an in vivo and in silico studies.

    abstract：:Different kinds of secondary metabolites present in the medicinal plants play an important role to alleviate different human ailments including neurodegenerative disorders such as Parkinson's, Alzheimer's, epilepsy and schizophrenia etc. Recently we have isolated and characterized a novel bioactive compound viz. 3-(3,...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1765875

    authors： Venkataramaiah C,Lakshmi Priya B,Rajendra W

    更新日期：2020-05-18 00:00:00

  • Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell.

    abstract：:Minidumbbell (MDB) is a newly found non-B DNA structure formed by short single-strand sequences. Up to now, three MDBs have been reported to form at neutral pH by sequences containing two repeats of TTTA, CCTG and CTTG. Among them, the thermodynamically less stable TTTA and CCTG MDBs have been proposed to be the struc...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1621211

    authors： Guo P,Lam SL

    更新日期：2020-04-01 00:00:00

  • 3D QSAR pharmacophore-based virtual screening for the identification of potential inhibitors of tyrosinase.

    abstract：:Tyrosinase plays an important role in melanin biosynthesis and protects skin against ultraviolet radiations. Functional deficiency of tyrosinase results in serious dermatological diseases. Tyrosinase also participates in neuromelanin formation in the human brain, which leads to neurodegeneration resulting in Parkinson...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1647287

    authors： Ghayas S,Ali Masood M,Parveen R,Aquib M,Farooq MA,Banerjee P,Sambhare S,Bavi R

    更新日期：2020-07-01 00:00:00

  • In-silico analysis of Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum through molecular modeling, docking, and dynamics simulation study.

    abstract：:Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1790036

    authors： Dhal AK,Pani A,Yun SI,Mahapatra RK

    更新日期：2020-07-07 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

  • Two polyphenols with diverse mechanisms towards amyloidosis: differential modulation of the fibrillation pathway of human lysozyme by curcumin and EGCG.

    abstract：:The effect of two widely used polyphenols, curcumin and EGCG was investigated on the amyloid fibrillogenesis of the well-characterized model protein human lysozyme (HuL), associated with non-neuropathic systemic amyloidosis, towards exploring their efficacy as modulators of HuL amyloid aggregation and toxicity and unr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1860824

    authors： Zaidi FK,Bhat R

    更新日期：2020-12-17 00:00:00

  • Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.

    abstract：:Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of fre...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2012.698244

    authors： Chen C,Huang Y,Xiao Y

    更新日期：2013-01-01 00:00:00

  • Screening of phytochemicals as potent inhibitor of 3-chymotrypsin and papain-like proteases of SARS-CoV2: an in silico approach to combat COVID-19.

    abstract：:COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to co...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1835729

    authors： Swargiary A,Mahmud S,Saleh MA

    更新日期：2020-10-22 00:00:00

  • Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays.

    abstract：:Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three differ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2017.1404934

    authors： Sutthibutpong T,Rattanarojpong T,Khunrae P

    更新日期：2018-11-01 00:00:00

  • Determination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation.

    abstract：:Rho-associated protein kinases (ROCKs) are a member of the serine/threonine protein kinase family and potential therapeutic target for various diseases. This enzyme has two isoforms, Rho-associated protein kinase I (ROCKI) and Rho-associated protein kinase II (ROCKII). They share an overall 65% homology in all amino a...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1491420

    authors： Bayel Secinti B,Tatar G,Taskin Tok T

    更新日期：2019-06-01 00:00:00

  • Methylglyoxal modification reduces the sensitivity of hen egg white lysozyme to stress-induced aggregation: Insight into the anti-amyloidogenic property of α-dicarbonyl compound.

    abstract：:The reactive α-oxoaldehyde, methylglyoxal reacts with different proteins to form Advanced Glycation End Products (AGEs) through Maillard reaction. Its level increases significantly in diabetic condition. Here, we have investigated the effect of different concentrations of methylglyoxal (200-400 µM) on the monomeric pr...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1702589

    authors： Banerjee S

    更新日期：2020-11-01 00:00:00

  • Effect of CTerm of human albumin on the aggregation propensity of Aβ1-42 peptide: a potential of mean force study.

    abstract：:Alzheimer's disease (AD) is the most common progressive neurodegenerative brain disorder. It is characterized by the presence of extracellular aggregated fibrillary form of amyloid beta (Aβ) peptide and intraneuronal neurofibrillary tangles caused by the hyperphosphorylation of tau protein. Monomeric form of Aβ peptid...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1730970

    authors： Dutta N,Borah P,Mattaparthi VSK

    更新日期：2020-03-02 00:00:00

  • Proposing a fungal metabolite-flaviolin as a potential inhibitor of 3CLpro of novel coronavirus SARS-CoV-2 identified using docking and molecular dynamics.

    abstract：:The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar virus, SA...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1813202

    authors： Rao P,Shukla A,Parmar P,Rawal RM,Patel BV,Saraf M,Goswami D

    更新日期：2020-09-02 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

  • Structural insight into HIV-1 reverse transcription initiation in MAL-like templates (CRF01_AE, subtype G and CRF02_AG).

    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

    pub_type： 杂志文章

    doi：10.1080/07391102.2014.884938

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

    更新日期：2015-01-01 00:00:00

  • Determination of the complete correlation between the sugar ring puckers and 5'-exocyclic group rotamers in conformationally-flexible nucleic acid components from NMR study.

    abstract：:Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations show...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1984.10507558

    authors： Remin M

    更新日期：1984-08-01 00:00:00

  • The formation of parallel RNA-RNA duplexes in vitro.

    abstract：:Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1995.10508860

    authors： Tchurikov NA,Ponomarenko NA,Golova YB,Chernov BK

    更新日期：1995-12-01 00:00:00

  • Salt-induced conformational transition of poly(d2NH2A-dT) studied by ultraviolet resonance Raman spectroscopy.

    abstract：:The conformational changes of poly(d2NH2A-dT) in aqueous solution, induced by increasing the NaCl concentration from 0.1M to 4M, have been monitored by ultraviolet resonance Raman spectroscopy, in using the 222-, 257- and 281 nm excitation wavelengths. These changes have been interpreted in comparing the polymer spect...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1992.10508637

    authors： Mojzes P,Chinsky L,Turpin PY,Miskovsky P

    更新日期：1992-08-01 00:00:00

  • Dancing retro: solution structure and micelle interactions of the retro-SH3-domain, retro-SHH-'Bergerac'.

    abstract：:A protein with the reversed direction of its polypeptide chain, retro-SHH, was analyzed by several spectroscopic techniques including circular dichroism and high-resolution NMR to understand its solution structure and structural consequences of interaction with the micelles formed by the zwitterionic detergent dodecyl...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2012.762724

    authors： Kutyshenko VP,Prokhorov DA,Molochkov NV,Sharapov MG,Kolesnikov I,Uversky VN

    更新日期：2014-01-01 00:00:00

  • Structural analysis of human lysozyme using molecular dynamics simulations.

    abstract：:In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, s...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2006.10507115

    authors： Liu HL,Wu YC,Zhao JH,Fang HW,Ho Y

    更新日期：2006-12-01 00:00:00

  • Structural and biological study of synthesized anthraquinone series of compounds with sulfonamide feature.

    abstract：:1, 4 and 5, 8-Positions as well as type of functionalities on these positions at anthraquinone-9, 10-dione are proposed to be significant for anticancer activity. Therefore, keeping this into consideration, a series of 1-substituted anthraquinone-based compounds are designed, synthesized, characterized and biologicall...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2018.1552198

    authors： Awasthi P,Vatsal M,Sharma A

    更新日期：2019-10-01 00:00:00

  • Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study.

    abstract：:Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2021.1872418

    authors： Mahmoudi Gomari M,Rostami N,Omidi-Ardali H,Arab SS

    更新日期：2021-01-21 00:00:00

  • Efficiency of coaxial stacking depends on the DNA duplex structure.

    abstract：:Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear r...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2003.10506940

    authors： Pyshnyi DV,Goldberg EL,Ivanova EM

    更新日期：2003-12-01 00:00:00