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 of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it. Communicated by Ramaswamy H. Sarma.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Mahmoudi Gomari M,Rostami N,Omidi-Ardali H,Arab SSdoi
10.1080/07391102.2021.1872418subject
Has Abstractpub_date
2021-01-21 00:00:00pages
1-9eissn
0739-1102issn
1538-0254pub_type
杂志文章abstract::Quasi-palindromic sequences (AT) X N12(AT) Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1532320
更新日期:2019-09-01 00:00:00
abstract::PPARα and PPARγ play important roles in regulating glucose and lipid metabolism. In recent years, the development of dual PPAR agonists has become a hot topic in the field of anti-diabetic medicinal chemistry. The dual PPARα/γ agonists can both improve metabolism and reduce side effects caused by single drugs, and has...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1745279
更新日期:2020-04-01 00:00:00
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 bindi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506987
更新日期:2004-08-01 00:00:00
abstract::Poly(dA-dT).poly(dA-dT) can adopt the B- and D- forms in the fibrous state. Theoretical energy calculations and fiber diffraction analyses suggest that there can be three structural models of poly(dA-dT).poly(dA-dT) in each of these two forms viz right and left-handed Watson Crick models and left-handed Hoogsteen--a t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507450
更新日期:1983-10-01 00:00:00
abstract::Tumor suppressor proteins play a crucial role in cell cycle regulation. Retinoblastoma protein (pRB) is one among them which regulates G1-S transition by binding with transcription factors. The activity of pRB is deregulated by cyclin dependent kinases-mediated hyper-phosphorylation and also due to cancer-derived muta...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.732345
更新日期:2013-01-01 00:00:00
abstract::The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506949
更新日期:2004-02-01 00:00:00
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
更新日期:2017-08-01 00:00:00
abstract::The World Health Organization has classified the COVID-19 outbreak a pandemic which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and declared it a global health emergency. Repurposing drugs with minimum side effects are one approach to quickly respond in attempt to prevent the spread of CO...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1863265
更新日期:2020-12-27 00:00:00
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
更新日期:2019-04-01 00:00:00
abstract::We have analysed S1 sensitivity of SV40 minichromosomes isolated from the nuclei of infected cells at the late stage of infection. We show that a fraction of purified minichromosomes is sensitive towards double-strand cleavage by S1 nuclease. The pattern of specific cleavage reminiscent of that found for subcloned fra...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10506522
更新日期:1989-04-01 00:00:00
abstract::A modelling procedure has been utilized to obtain a preliminary three-dimensional structural model for the bacteriophage IKe DNA binding protein (IKe-DBP) based on the known high resolution X-ray diffraction structure of a functionally related protein (G5BP) from bacteriophage fd. The degree of structural homology obs...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10507683
更新日期:1987-04-01 00:00:00
abstract::The N-terminal receiver domain of NtrC is the molecular switch in the two-component signal transduction. It is the first protein where structures of both the active (phosphyroylated) and inactive (unphosphyroylated) states are determined experimentally. Phosphorylation of the NtrC at the active site induces large stru...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2006.10507075
更新日期:2006-04-01 00:00:00
abstract::Calcium/calmodulin-dependent protein kinase IV (CaMKIV) is a multifunctional enzyme which belongs to the Ser/Thr kinase family. CaMKIV plays important role in varieties of biological processes such as gene expression regulation, memory consolidation, bone growth, T-cell maturation, sperm motility, regulation of microt...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1150203
更新日期:2017-02-01 00:00:00
abstract::Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with mole...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1632225
更新日期:2020-05-01 00:00:00
abstract::The signaling response of TLR2 to ligands has always been as a homodimer or in heterodimerization with TLR1/TLR6. The Toll/Interleukin-1 Receptor (TIR) domain of the TLR cytoplasmic region regulates the dimerization and interactions with adaptor molecules to build an active signaling complex. To understand the conserv...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1786457
更新日期:2020-07-08 00:00:00
abstract::Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2',5' or 3',5' type. It is shown that a nucleotide which is "compact" in 3',5' nucleic acids is rendered "extended" and vice versa for a given sugar pucker. It is interesting that t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508249
更新日期:1998-10-01 00:00:00
abstract::Lymphatic filariasis is a debilitating vector borne parasitic disease that infects human lymphatic system by nematode Brugia malayi. Currently available anti-filarial drugs are effective only on the larval stages of parasite. So far, no effective drugs are available for humans to treat filarial infections. In this reg...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1427633
更新日期:2019-02-01 00:00:00
abstract::Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1837680
更新日期:2020-10-23 00:00:00
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
pub_type: 杂志文章
doi:10.1080/07391102.2020.1869096
更新日期:2021-01-08 00:00:00
abstract::Abstract The forces that direct protein folding lead naturally to native proteins and protein domains that are typically, to a first approximation, globular-spherical and compact, with a relatively clear distinction between the hydrophobic inside and polar outside. The near-universality of these features of protein ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506607
更新日期:2000-01-01 00:00:00
abstract::A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508232
更新日期:1998-08-01 00:00:00
abstract::Matriptase is a serine protease associated with a wide variety of human tumors and carcinoma progression. Up to now, many promising anti-cancer drugs have been developed. However, the detailed structure-function relationship between inhibitors and matriptase remains elusive. In this work, molecular dynamics simulation...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1160259
更新日期:2017-03-01 00:00:00
abstract::We attempt to give an alternate point of view of the analysis by Roterman et al. (J. Biolmol. Struct. Dyn. 7,415 (1989]. In particular, we argue for the use of flexible geometry and explicit inclusion of solvent effects in analyzing phi, psi maps of peptides. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1991.10507872
更新日期:1991-06-01 00:00:00
abstract::The functional aspect of several mycobacterium proteins annotated as hypothetical are yet to be discovered. In the present investigation, in silico approaches were used to predict the biological function of some of the unknown Mtb proteins, which were further validated by wet lab experiments. After screening thousands...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1174738
更新日期:2017-05-01 00:00:00
abstract::The effect of ligand interacting with native DNA by two types on the parameters of helix-coil transition in homopolymers is considered using the most probable distribution method (Yu.S. Lazurkin et al., Biopolymers 1970). It is shown that at a small relative concentration of ligand the melting enthalpy (delta H) of DN...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1990.10507793
更新日期:1990-08-01 00:00:00
abstract::In this work, an attempt has been made to study the interaction of four taiwaniaquinoids with fat mass and obesity-associated protein (FTO) by UV-vis absorption, fluorescence spectroscopy, and molecular docking techniques. The results indicated that taiwaniaquinoids effectively quenched the intrinsic fluorescence of F...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1249957
更新日期:2017-11-01 00:00:00
abstract::The inhibitory efficacy of two substituted coumarin derivatives on the activity of neurodegenerative enzyme acetylcholinesterase (AChE) was assessed in aqueous buffer as well as in the presence of human serum albumin (HSA) and compared against standard cholinergic AD drug, Donepezil (DON). The experimental data reveal...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1465853
更新日期:2019-04-01 00:00:00
abstract::Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, lin...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507587
更新日期:1984-12-01 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
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
pub_type: 杂志文章
doi:10.1080/07391102.2014.997797
更新日期:2015-01-01 00:00:00