Abstract:
:The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and 10.0, respectively. Each replica was run for 300 ns. The structural and thermodynamic characters of alpha syn12 peptide were studied based on the distributions of backbone dihedral angles, the free energy surface, and the stability of different type structure and the favorite conformations of the peptide. The results showed that the simulation at pH = 10.0 produced more sampling in alpha region than the simulation at pH = 7.0. The temperature changes from 283 K to 308 K result in negligible effects on the distributions of backbone dihedral angle. The beta hairpin conformation with Turn(9-6) and four hydrogen bonds (HB(4-11), HB(6-9), HB(9-6) and HB(11-4)) is the lowest free energy state in the simulation at pH = 7.0. However, for the simulation at pH = 10.0, the lowest free energy state corresponds to a structure with Turn(9-6) and two hydrogen bonds (HB(6-10) and HB(10-6)) induced by an overly strong residue-residue interaction effect between lysine residues. For the simulation at pH = 7.0, the free energy change of the alpha-syn12 peptide from the unfolded state to the beta hairpin state was in good agreement with the experiments and molecular dynamics simulation results for the other beta-peptides, the beta hairpin state of the alpha-syn12 peptide included the conformations that not only the Turn(9-6) is formed, but also the terminus are closed together in space. However, the subtle balances between lysine-lysine interactions and lysine-solvent interaction are disrupted in the simulation at pH = 10.0, which induced the assembly of lysine residues, the beta hairpin conformation is destabilized by the deprotonation of the Lys side chain. This study can help us to understand the conformation changes and the thermodynamic character of alpha;-syn12 peptide at atomic level induced by changing pH and temperature, which is propitious to reveal the nosogenesis of Parkinson disease. In our knowledge, this is the first report to study the influence of pH and temperature on isolated alpha-syn12 peptide in water by T-REMD.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Cao Z,Liu L,Wang Jdoi
10.1080/07391102.2010.10507364subject
Has Abstractpub_date
2010-12-01 00:00:00pages
343-53issue
3eissn
0739-1102issn
1538-0254pii
c4303/Effects-of-pH-and-Temperature-on-the-Structujournal_volume
28pub_type
杂志文章abstract::The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH3O)2(POS)]-, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calc...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1997.10508149
更新日期:1997-02-01 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::The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-t...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506591
更新日期:2000-06-01 00:00:00
abstract::The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from natural plant sources is an area of immense potential. The curre...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1762743
更新日期:2020-05-12 00:00:00
abstract::The conformational space available to GnRH and lGnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calcu...
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
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
更新日期:2020-03-02 00:00:00
abstract::Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1737233
更新日期:2020-03-11 00:00:00
abstract::Visible and near infrared magnetic circular dichroism (MCD) spectra of heme proteins and enzymes as well as those of a protein-free heme bound to 2-methylimidazole were recorded and compared at 4.2 K in unrelaxed metastable and relaxed equilibrium heme stereochemistry. The relaxed and unrelaxed stereochemistries of a ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10507761
更新日期:1989-08-01 00:00:00
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
更新日期:2009-10-01 00:00:00
abstract::Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the hum...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1426044
更新日期:2019-02-01 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::Interaction of levocabastine with human serum albumin (HSA) is investigated by applying fluorescence spectroscopy, circular dichroism spectroscopy and molecular docking methods. Levocabastine is an important drug in treatment of allergy and currently a target drug for drug repurposing to treat other diseases like vern...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1750486
更新日期:2020-04-20 00:00:00
abstract::We determined the binding sites of curcumin (cur), resveratrol (res), and genistein (gen) with milk β-lactoglobulin (β-LG) at physiological conditions. Fourier transform infrared spectroscopy, circular dichroism, and fluorescence spectroscopic methods as well as molecular modeling were used to determine the binding of...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.742461
更新日期:2013-12-01 00:00:00
abstract::NPC1 is a 25-exon gene located on the long arm of chromosome 18q11.2 and encodes NPC1, a transmembrane protein comprising 1278 amino acid residues. Mutations in the NPC1 gene can cause Niemann-Pick disease type C (NP-C), a rare autosomal-recessive neurovisceral disease. We assessed mutant protein folding using compute...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1664324
更新日期:2020-08-01 00:00:00
abstract::Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1985.10508414
更新日期:1985-10-01 00:00:00
abstract::Doublesex and Mab-3-related transcription factor (DMRT) gene family is widely known for its involvement in sex determination and/or differentiation among different phyla. In this study, we identify eight DMRT genes in the cephalochordate amphioxus, a protochordate holding a key phylogenetic position. The eight DMRTs c...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.677770
更新日期:2012-01-01 00:00:00
abstract::The interaction of Δ- and Λ-[Ru(phen)2DPPZ]2+ (DPPZ = dipyrido[3,2-a:2', 3'-c]phenazine, phen = phenanthroline) with a G-quadruplex formed from 5'-G2T2G2TGTG2T2G2-3'(15-mer) was investigated. The well-known enhancement of luminescence intensity (the 'light-switch' effect) was observed for the [Ru(phen)2DPPZ]2+ complex...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1345324
更新日期:2018-06-01 00:00:00
abstract::Understanding, at the molecular level, the effect of AMPs on biological membranes is of crucial importance given the increasing number of multidrug-resistant bacteria. Being part of an ancient type of innate immunity system, AMPs have emerged as a potential solution for which bacteria have not developed resistance. Tr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1867640
更新日期:2021-01-05 00:00:00
abstract::Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1754918
更新日期:2020-04-23 00:00:00
abstract::The thermal denaturation of the synthetic high molecular weight double stranded polynucleotide poly(dA-dT) x poly(dA-dT) has been studied in aqueous buffered solution (Tris 1.0 mM; pH 7.8+/-0.2) in the presence of increasing concentrations of either Ni(2+) (borderline cation) or Cd(2+) (soft cation) at four different ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2007.10507157
更新日期:2007-08-01 00:00:00
abstract::Polar mutations in transmembrane alpha helices may alter the structural details of the hydrophobic sequences and control intermolecular contacts. We have performed molecular dynamics simulations on the transmembrane domain of the proto-oncogenic and the oncogenic forms of the Neu receptor in a fluid DMPC bilayer to te...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2005.10507050
更新日期:2005-08-01 00:00:00
abstract::The 9-aminoacridine-DNA binding curve is analyzed in two ways: with polyelectrolyte effects neglected and with polyelectrolyte effects included. It is found that the analysis which includes polyelectrolyte effects is consistent with the violation of neighbor exclusion displayed by diacridine complexes as observed by A...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1991.10507861
更新日期:1991-04-01 00:00:00
abstract::We have applied random-search, energy minimization and molecular dynamics simulations to investigate the structural aspects of the interaction of N-acetyl-L-prolyl-D-alanyl-L-alanine-N'-methylamide with Ca2+. Spectral data on related peptides had suggested that the beta-turn conformation might be a prerequisite for th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10508647
更新日期:1992-10-01 00:00:00
abstract::Medicinal herbs have proved along history to be a source of multiple cures. In this paper, we demonstrate how hydroxychloroquine can act as a good inhibitor of SARS-CoV-2 Spike protein receptor-binding-domain using molecular docking studies. We also unveil how hydroxychloroquine can interfere in the prevention of Lys3...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1796809
更新日期:2020-07-22 00:00:00
abstract::COVID-19 is an infectious pandemic caused by the SARS-CoV-2 virus. The critical components of SARS-CoV-2 are the spike protein (S-protein) and the main protease (Mpro). Mpro is required for the maturation of the various polyproteins involved in replication and transcription. S-protein helps the SARS-CoV-2 to enter the...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1842246
更新日期:2020-11-05 00:00:00
abstract::Our earlier study on the nucleosomes containing TBP binding sites (TATA boxes) indicated that generally the same sequence, which harbors the TATA box, encodes simultaneously an alternative rotational setting of the box, so that the TATA element is either exposed (position "minor groove out") or hidden in position "min...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1134348
更新日期:2016-12-01 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::The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major worldwide public health emergency that has infected over 8 million people. Spike glycoprotein, especially the partially open state of S1 subunit, in SARS-CoV-2 is considered vital for its infection with human host cell. However, the mech...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1802338
更新日期:2020-08-04 00:00:00
abstract::Resonance Raman spectra with Q-band excitation are reported for microperoxidase-11, the cytochrome c analog. Spectra were acquired in the mid-frequency range for the oxidized, and reduced forms of the undecapeptide, as well as for the imidazole and carbonyl complexes. Oxidation and spin state marker bands of the undec...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508999
更新日期:1998-06-01 00:00:00
abstract::The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507467
更新日期:1983-12-01 00:00:00