当前位置： SCI文献检索 > JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS期刊下所有文献 > Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays.

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 different sites to the thermostability. The first mutation was to replace an unstable negatively charged residue at a surface beta turn near the active site (D32G) by a hydrophobic residue. The second mutation was to create a disulphide bond (S100C/N147C) establishing a strong connection between an alpha helix and a distal beta hairpin associated with the thermally sensitive Thumb loop, and the third mutation add an extra hydrogen bond (A155S) to the same alpha helix. From the MD simulations performed, MM/PBSA energy calculations of the unfolding energy were in a good agreement with the enzyme activities measured from the experiment, as all mutated structures demonstrated the improved thermostability, especially the S100C/N147C proved to be the most stable mutant both by the simulations and the experiment. Local conformational analysis at the catalytic sites and the xylan access region also suggested that mutated xyn11A structures could accommodate xylan binding. However, the analysis of global unfolding pathways showed that structural disruptions at the beta sheet regions near the N-terminal were still imminent. These findings could provide the insight on the molecular mechanisms underlying the enhanced thermostability due to mutagenesis and changes in the protein unfolding pathways for further protein engineering of the GH11 family xylanase enzymes.

journal_name

J Biomol Struct Dyn

journal_title

Journal of biomolecular structure & dynamics

authors

Sutthibutpong T,Rattanarojpong T,Khunrae P

doi

10.1080/07391102.2017.1404934

subject

Has Abstract

pub_date

2018-11-01 00:00:00

pages

3978-3992

issue

15

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
  • Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure.

    abstract：:Communicated by Ramaswamy H. Sarma. ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 信件

    doi：10.1080/07391102.2019.1591306

    authors： Kargatov AM,Efimov AV

    更新日期：2020-03-01 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

  • 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

  • Structural analysis, molecular docking and molecular dynamics simulations of G-protein-coupled receptor (kisspeptin) in fish.

    abstract：:Kisspeptins are neuropeptide that has emerged as an essential gatekeeper for reproduction and onset of puberty in higher vertebrates including fish. In present study, structural analysis, molecular docking and molecular dynamics simulations of kisspeptin receptor (kiss2r) were carried out, which is a G-protein-coupled...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1633407

    authors： Rather MA,Dutta S,Guttula PK,Dhandare BC,Yusufzai SI,Zafar MI

    更新日期：2020-05-01 00:00:00

  • Novel quinazolin-sulfonamid derivatives: synthesis, characterization, biological evaluation, and molecular docking studies.

    abstract：:In the design of novel drugs, the formation of hybrid molecules via the combination of several pharmacophores can give rise to compounds with interesting biochemical profiles. A series of novel quinazolin-sulfonamid derivatives (9a-m) were synthesized, characterized and evaluated for their in vitro antidiabetic, antic...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1847193

    authors： Sepehri N,Mohammadi-Khanaposhtani M,Asemanipoor N,Hosseini S,Biglar M,Larijani B,Mahdavi M,Hamedifar H,Taslimi P,Sadeghian N,Norizadehtazehkand M,Gulcin I

    更新日期：2020-11-23 00:00:00

  • Design, synthesis and biological evaluation of selected 3-[3-(amino) propoxy] benzenamines as acetylcholinesterase inhibitors.

    abstract：:The present paper describes design, synthesis, and biological evaluation of a series of some 3-[3-(amino)propoxy]benzenamines as acetylcholinesterase inhibitors using mice as a model and piracetam as a reference drug. The structures of these compounds were confirmed by spectral analysis and compounds were tested for m...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1220330

    authors： Malik R,Gupta R,Srivastava S,Choudhary BS,Sharma M

    更新日期：2017-08-01 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

  • Transcription factors operate TATA switches via rotational remodeling of local columnar chromatin structure.

    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

    authors： Trifonov EN

    更新日期：2016-12-01 00:00:00

  • Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents.

    abstract：:Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1688196

    authors： Pan Z,Wang Y,Gu X,Wang J,Cheng M

    更新日期：2020-10-01 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

  • New heat shock protein (Hsp90) inhibitors, designed by pharmacophore modeling and virtual screening: synthesis, biological evaluation and molecular dynamics studies.

    abstract：:Inhibition of heat shock protein 90 (Hsp90) is known to be a significantly effective strategy in cancer therapy. Here, pyrazolopyranopyrimidine derivatives were characterized as new Hsp90 inhibitors. The molecules' key structure (ZINC02819805) was determined by utilizing a pharmacophore model virtual screening workflo...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1660216

    authors： Abbasi M,Amanlou M,Aghaei M,Bakherad M,Doosti R,Sadeghi-Aliabadi H

    更新日期：2020-08-01 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

  • Acid-induced structural changes of a mouse IgG2a monoclonal antibody (MN12) studied by transient electric birefringence measurement.

    abstract：:Acid-induced structural changes of a mouse IgG2a monoclonal antibody (MN12) as indicated by Jiskoot et al. (Eur. J. Biochem. 201,223-232 (1991)) were studied by measuring the transient electric birefringence of MN12 in aqueous solution and in glycerol-water mixtures at different pH conditions. A multi-exponential anal...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1992.10507972

    authors： van Haeringen B,Jiskoot W,van Grondelle R,Bloemendal M

    更新日期：1992-04-01 00:00:00

  • Molecular dynamics simulation and molecular docking studies of 1,4-Dihydropyridines as P-glycoprotein's allosteric inhibitors.

    abstract：:P-glycoprotein (P-gp) is a main factor contributing to multidrug resistance. The effect of this transporter protein on limiting the effectiveness of chemotherapy has been shown by various studies. In a previous report, we synthesized some 14-dihydropyridine (DHP) derivatives as inhibitors of human P-gp. In the present...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2016.1268976

    authors： Shahraki O,Zargari F,Edraki N,Khoshneviszadeh M,Firuzi O,Miri R

    更新日期：2018-01-01 00:00:00

  • The effect of spermine binding on the reactivity of DNA towards carcinogenic alkylating agents.

    abstract：:The effect of spermine binding on the electrostatic potential of DNA is evaluated. The calculations are performed for the essential reactive sites, atoms N7 and O6 of guanine, N3 and N7 of adenine, of the nucleic acid and for its surface envelope. An important weakening of the potential is found affecting all the impo...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1985.10508433

    authors： Zakrzewska K,Pullman B

    更新日期：1985-12-01 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

  • Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2.

    abstract：:Drug re-purposing might be a fast and efficient way of drug development against the novel coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We applied a bioinformatics approach using molecular dynamics and docking to identify FDA-approved drugs that can be re-purposed to ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2020.1811773

    authors： Chandel V,Sharma PP,Raj S,Choudhari R,Rathi B,Kumar D

    更新日期：2020-08-24 00:00:00

  • DNA-drug interaction measurements using surface plasmon resonance.

    abstract：:The interactions of the drugs 2,7-bis[(diethylamino)-ethoxy]-fluoren-9-one dihydrochloride (Tilorone), 2,7-bis[(dipropylamino)-acetamido]-fluoren-9-one dihydrochloride (FA-2), 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole trihydrochloride (Hoechst 33258), and hematoporphyrin IX derivative (H...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1998.10508239

    authors： Bischoff G,Bischoff R,Birch-Hirschfeld E,Gromann U,Lindau S,Meister WV,de A Bambirra S,Bohley C,Hoffmann S

    更新日期：1998-10-01 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

  • An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies.

    abstract：:Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work atte...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1567388

    authors： Kashyap K,Kakkar R

    更新日期：2020-01-01 00:00:00

  • Interaction of Piscidin-1 with zwitterionic versus anionic membranes: a comparative molecular dynamics study.

    abstract：:Plasma membrane of each micro-organism has a unique set of lipid composition as a consequence of the environmental adaptation or a response to exposure to antimicrobial peptides (AMPs) as antibiotic agents. Understanding the relationship between lipid composition and action of antimicrobial peptides or considering how...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2012.737295

    authors： Rahmanpour A,Ghahremanpour MM,Mehrnejad F,Moghaddam ME

    更新日期：2013-12-01 00:00:00

  • Computer analysis of R-looped DNA from electron micrographs.

    abstract：:The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1986.10508495

    authors： Golovanov EuI,Kalambet YuA,Auezova LJ,Alexandrov AA

    更新日期：1986-06-01 00:00:00

  • In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database.

    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

    authors： Feng XY,Ding TT,Liu YY,Xu WR,Cheng XC

    更新日期：2020-04-01 00:00:00

  • Determination of the backbone mobility of ribonuclease T1 and its 2'GMP complex using molecular dynamics simulations and NMR relaxation data.

    abstract：:The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.1994.10508074

    authors： Fushman D,Ohlenschläger O,Rüterjans H

    更新日期：1994-06-01 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

  • Identification of Pak1 inhibitors using water thermodynamic analysis.

    abstract：:p21-activated kinases (Paks) play an integral component in various cellular diverse processes. The full activation of Pak is dependent upon several serine residues present in the N-terminal region, a threonine present at the activation loop, and finally the phosphorylation of these residues ensure the complete activat...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1567393

    authors： Biswal J,Jayaprakash P,Suresh Kumar R,Venkatraman G,Poopandi S,Rangasamy R,Jeyaraman J

    更新日期：2020-01-01 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

  • How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

    abstract：:In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pat...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2015.1046936

    authors： Brovarets' OO,Hovorun DM

    更新日期：2015-01-01 00:00:00

  • Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches.

    abstract：:NAD(P)H: quinone oxidoreductase 1 (NQO1) inhibitors are proved as promising therapeutic agents against cancer. This study is to determine potent NAD(P)H-dependent NQO1 inhibitors with new scaffold. Pharmacophore-based three-dimensional (3D) QSAR model has been built based on 45 NQO1 inhibitors reported in the literatu...

    journal_title：Journal of biomolecular structure & dynamics

    pub_type： 杂志文章

    doi：10.1080/07391102.2019.1585291

    authors： Selvakumar R,Anantha Krishnan D,Ramakrishnan C,Velmurugan D,Gunasekaran K

    更新日期：2020-02-01 00:00:00

  • Unusual stability exhibited by (AT)XN12(AT)Y motif associated with high fetal hemoglobin levels.

    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

    authors： Roy K,Mahendru S,Kukreti R,Kukreti S

    更新日期：2019-09-01 00:00:00