The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis

Silva, Sérgio Bergamachi; Pinheiro, Matheus Pinto; Fuzo, Carlos Alessandro; Silva, Samuel Reghim; Ferreira, Tatiane Lopes; Lourenzoni, Marcos Roberto; Nonato, Maria Cristina; Vieira, Davi Serradella; Ward, Richard J.

doi:10.1016/j.ijbiomac.2017.01.054

Cited by 14 publications

(12 citation statements)

References 57 publications

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“…To analyze the adsorption between peptides and lipid bilayer we used the Interaction Potential Energy (IPE), which can be defined as the total interaction energy between two groups, (the sum of electrostatic and van der Waals contributions), and it was computed according to the equation:IPEnormali,normalj=∑iNi∑normalj≠normaliNjVvdW(rij)+VEle(rij), where IPE i,j is the interaction energy between a group of atoms i and a group of atoms j , and N i and N j are the total number of atoms on groups i and j , VEle and VvdW are the terms corresponding to electrostatic and van der Waals contribution, respectively. This parameter is often used to evaluate interaction energies in protein–ligand and protein–protein systems [44], but can also be applied to quantify interaction between specific amino acids and the surrounding molecules [45]. For IPE calculations, all peptide atoms were considered in the calculation.…”

Section: Methodsmentioning

confidence: 99%

Potent and Broad-Spectrum Antimicrobial Activity of Analogs from the Scorpion Peptide Stigmurin

Amorim-Carmo

Daniele-Silva

Parente

et al. 2019

IJMS

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Scorpion venom constitutes a rich source of biologically active compounds with high potential for therapeutic and biotechnological applications that can be used as prototypes for the design of new drugs. The aim of this study was to characterize the structural conformation, evaluate the antimicrobial activity, and gain insight into the possible action mechanism underlying it, for two new analog peptides of the scorpion peptide Stigmurin, named StigA25 and StigA31. The amino acid substitutions in the native sequence for lysine residues resulted in peptides with higher positive net charge and hydrophobicity, with an increase in the theoretical helical content. StigA25 and StigA31 showed the capacity to modify their structural conformation according to the environment, and were stable to pH and temperature variation—results similar to the native peptide. Both analog peptides demonstrated broad-spectrum antimicrobial activity in vitro, showing an effect superior to that of the native peptide, being non-hemolytic at the biologically active concentrations. Therefore, this study demonstrates the therapeutic potential of the analog peptides from Stigmurin and the promising approach of rational drug design based on scorpion venom peptide to obtain new anti-infective agents.

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Section: Methodsmentioning

confidence: 99%

Potent and Broad-Spectrum Antimicrobial Activity of Analogs from the Scorpion Peptide Stigmurin

Amorim-Carmo

Daniele-Silva

Parente

et al. 2019

IJMS

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“…5B). However, a slight increase in RMSF values was observed for the N8Y mutant over positions 10 to 12, indicating that the neighboring residues were more flexible with Tyr at position 8 compared to Asn at the same position (15).…”

Section: Structural Comparisons and MD Simulations Of Wild-type Xynlc9 And Its Mutantsmentioning

confidence: 93%

“…The large cleft between the "finger" and the "palm" domains was regarded as the active site, with two catalytic glutamate residues (Glu78 and Glu172) residing on B6 and B4. A loop between β-strands B7 and B8 created the "thumb" domain, which was critical for controlling substrate access to the active site, while another loop between the B6 and B9 strands formed a "cord" that connected the "fingers" with the base of the "thumb" (15). The structural model of XynLC9 was used to identify functionally relevant residues and regions by comparing it to the structures of related GH11 xylanases that had superior catalytic activity and whose primary reaction products were X2 and/or X3.…”

Section: Selection Of Mutation Sites Based On the Structural Alignments Of Gh11 Xylanasesmentioning

confidence: 99%

Sequence- and structure-guided improvement of the catalytic performance of a GH11 family xylanase from Bacillus subtilis

Wang

Cao

Pedroso

et al. 2021

Journal of Biological Chemistry

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…Bununla birlikte sadece hipertermofillerde bulunduğu düşünülen özel bir protein sayesinde DNA'nın degrade olmaması söz konusudur. Tüm hipertermofiller ters DNA giraz olarak adlandırılan bir DNA topoizomeraz üretirler [11][12] [13].…”

Section: Termofilik Arkelerde Yüksek Sıcaklık Adaptasyonuunclassified

Diversity of thermophilic archaea and their biotechnological uses

Özkan¹,

Başbülbül²

2021

Biological Diversity and Conservation

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The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis

Cited by 14 publications

References 57 publications

Potent and Broad-Spectrum Antimicrobial Activity of Analogs from the Scorpion Peptide Stigmurin

Potent and Broad-Spectrum Antimicrobial Activity of Analogs from the Scorpion Peptide Stigmurin

Sequence- and structure-guided improvement of the catalytic performance of a GH11 family xylanase from Bacillus subtilis

Diversity of thermophilic archaea and their biotechnological uses

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