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, secondary structural stability, radius of gyration, accessible surface area, and hydrophobic contact of the hydrophobic core all show that ethanol tends to destabilize human lysozyme at high temperatures. It can be attributed to that higher temperatures result in the destruction of the native structure of this protein, leading to the exposure of the interior hydrophobic core. At this stage, ethanol plays a role to destroy this region by forming hydrophobic interactions between protein and solvent due to its lower polarity comparing to water. Such newly formed intermolecular interactions accelerate the unfolding of this protein, starting from the core between the alpha- and beta-domains. Our results are in good agreement with the previous hypothesis suggesting that the distortion of the hydrophobic core at the alpha- and beta-interface putatively results in the formation of the initial "seed" for amyloid fibril. Although the present results cannot directly be linked to fibril formation, they still provide valuable insights into amyloidosis of human lysozyme.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Liu HL,Wu YC,Zhao JH,Fang HW,Ho Ydoi
10.1080/07391102.2006.10507115subject
Has Abstractpub_date
2006-12-01 00:00:00pages
229-38issue
3eissn
0739-1102issn
1538-0254pii
d=3024&c=4216&p=15337&do=detailjournal_volume
24pub_type
杂志文章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
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abstract：:Multidrug efflux mechanism is the main cause of intrinsic drug resistance in bacteria. Mycobacterium multidrug resistant (MMR) protein belongs to small multidrug resistant family proteins (SMR), causing multidrug resistance to proton (H(+))-linked lipophilic cationic drug efflux across the cell membrane. In the presen...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2013.842185
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abstract：:We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1991.10507864
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2001.10506736
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1988.10506466
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abstract：:Communicated by Ramaswamy H. Sarma. ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 信件
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1985.10507605
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2000.10506574
更新日期：2000-04-01 00:00:00
abstract：:Supercoiling causes global twist of DNA structure and the supercoiled state has wide influence on conformational transition. A statistical mechanical approach was made for prediction of the transition probability to non-B DNA structures under torsional stress. A conditional partition function was defined as the sum ov...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1993.10507997
更新日期：1993-02-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2015.1073632
更新日期：2016-06-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1986.10507643
更新日期：1986-08-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2014.974211
更新日期：2015-01-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1985.10506322
更新日期：1985-02-01 00:00:00
abstract：:The Runt domain proteins are eukaryotic transcription factors that regulate major developmental pathways. All members of this family contain a highly-conserved sequence-specific DNA binding domain: the Runt domain (RD). Structural and biochemical studies have shown that the Runt domain undergoes a conformational trans...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2007.10507124
更新日期：2007-02-01 00:00:00
abstract：:The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2017.1368417
更新日期：2018-08-01 00:00:00
abstract：:As the number of available three dimensional coordinates of proteins increases, it is now recognized that proteins from different families and topologies are constructed from independent motifs. Detection of specific structural motifs within proteins aids in understanding their role and the mechanism of their operatio...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1992.10507955
更新日期：1992-02-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2020.1766572
更新日期：2020-05-20 00:00:00
abstract：:The potassium channel Kv1.3 is an important pharmacological target and the Kaliotoxin-type toxins (α-KTX-3 family) are its specific blockers. Here, we study the binding process of two kinds of Kaliotoxin-type toxins:BmKTX and its mutant (BmKTX-D33H) toward to Kv1.3 channel using MD simulation and umbrella sampling sim...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1760135
更新日期：2020-05-06 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2001.10506703
更新日期：2001-04-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
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更新日期：2020-03-02 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2014.968622
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2013.819788
更新日期：2014-01-01 00:00:00
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
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更新日期：2020-12-09 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2013.827132
更新日期：2014-01-01 00:00:00
abstract：:Communicated by Ramaswamy H. Sarma. ...
journal_title：Journal of biomolecular structure & dynamics
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abstract：:The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...
journal_title：Journal of biomolecular structure & dynamics
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更新日期：2021-01-08 00:00:00
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
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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
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2007.10507133
更新日期：2007-04-01 00:00:00
abstract：:Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in a...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2012.745821
更新日期：2014-01-01 00:00:00
