scholarly journals The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts

2017 ◽  
Vol 8 (4) ◽  
pp. 2868-2877 ◽  
Author(s):  
Christopher R. Walters ◽  
D. Miklos Szantai-Kis ◽  
Yitao Zhang ◽  
Zachary E. Reinert ◽  
W. Seth Horne ◽  
...  
Keyword(s):  
Protein Structure ◽  
Protein Stability ◽  
Peptide Bond ◽  
Single Atom ◽  
Polyproline Ii ◽  
Β Sheet

Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure.

Binding of glutamine to glutamine-binding protein from Escherichia coli induces changes in protein structure and increases protein stability

2004 ◽  
Vol 58 (1) ◽  
pp. 80-87 ◽  
Author(s):  
Sabato D'Auria ◽  
Andrea Scirè ◽  
Antonio Varriale ◽  
Viviana Scognamiglio ◽  
Maria Staiano ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Structure ◽  
Protein Stability ◽  
Binding Protein

scholarly journals A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260054
Author(s):  
Safayat Mahmud Khan ◽  
Ar-Rafi Md. Faisal ◽  
Tasnin Akter Nila ◽  
Nabila Nawar Binti ◽  
Md. Ismail Hosen ◽  
...  
Keyword(s):  
Protein Structure ◽  
T Cell ◽  
Protein Stability ◽  
In Silico ◽  
Catalytic Domain ◽  
Cell Lymphoma ◽  
Computational Study ◽  
Solvent Accessibility ◽  
T Cell Lymphoma ◽  
Post Translational Modification

PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5’ and 3’ untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.

scholarly journals Boosting protein stability with the computational design of β-sheet surfaces

2016 ◽  
Vol 25 (3) ◽  
pp. 702-710 ◽  
Author(s):  
Doo Nam Kim ◽  
Timothy M. Jacobs ◽  
Brian Kuhlman
Keyword(s):  
Protein Stability ◽  
Computational Design ◽  
Β Sheet

NMR and Mutagenesis Investigations of a Model Cis: Trans Peptide tsomerization Reaction: Xaa116-Pro117of Staphylococcal Nuclease and its Role in Protein Stability and Folding

1997 ◽  
Author(s):  
A.P. Hinck ◽  
W.F. Walkenhorst
Keyword(s):  
Protein Stability ◽  
Time Scale ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Peptide Bond ◽  
Staphylococcal Nuclease ◽  
Isomerization Reaction ◽  
Molecular Heterogeneity ◽  
Proline Isomerization ◽  
Imino Acids

The slow rates of peptide bond isomerization in imino acids and the substantial population of the cis peptide bond isomer in Xaa-Pro linkages in peptides were first recognized in NMR studies of proline-containing model compounds (Maia et al., 1971). The important role of this isomerization in protein stability and folding (reviewed by Kim and Baldwin, 1982, 1990; Schmid, 1993) were recognized several years later (Brandts et al., 1975) and the biological relevance of this process was substantiated by the discovery of a ubiquitous enzyme that catalyzes Xaa-Pro peptide bond isomerization (Fischer et al., 1984, 1989; Takahashi et al., 1989). The strict evolutionary conservation of some prolyl residues and the observation that the kinetics of interconversion between alternative functional forms of some systems is consistent with the time scale of proline isomerization suggest that proline isomerization may play a wide role in protein structure and function. Suggestive examples include the sodium pump of Escherichia coli, the disulfide isomerase/thioredoxin class of enzymes, concanavalin A, and bovine prothrornbin fragment I (Brown et al., 1977; Marsh et al, 1979; Dunker, 1982; Brandland Deber, 1986; Langsetmo et al, 1989). NMR spectroscopy is one of the most suitable tools for studying this isomerization reaction. The rates generally are slow on the time scale of NMR chemical shifts but, in favorable cases, are comparable to longitudinal relaxation rates so that the isomerization process can be investigated by chemical exchange spectroscopy. NMR data obtained on calbindin D9k (Chazin et al., 1989), insulin (Higgins et al., 1988), and staphylococcal nuclease (nuclease) as discussed below have shown that each exists in solution under native conditions as a mixture of slowly exchanging conformers. The fact that dynamic molecular heterogeneity in nuclease was first observed in the laboratory of Oleg Jardetzky, as manifested by splitting of the histidyl 1H ε1 resonance from His46 in one-dimensional 1H NMR spectra recorded at 100 MHz (Markley et al., 1970), makes this topic particularly appropriate to a volume celebrating his scientific contributions.

SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES

2012 ◽  
Vol 10 (02) ◽  
pp. 1241003 ◽  
Author(s):  
EVGENIY AKSIANOV ◽  
ANDREI ALEXEEVSKI
Keyword(s):  
Protein Structure ◽  
Three Dimensional ◽  
Structural Features ◽  
Protein Domain ◽  
Structural Units ◽  
Protein Structure Classification ◽  
Β Sheets ◽  
Β Sheet ◽  
Explicit Determination

The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a “β-sheet map,” a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service http://mouse.belozersky.msu.ru/sheep allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features.

scholarly journals BPTI folding revisited: switching a disulfide into methylene thioacetal reveals a previously hidden path

2018 ◽  
Vol 9 (21) ◽  
pp. 4814-4820 ◽  
Author(s):  
Reem Mousa ◽  
Shifra Lansky ◽  
Gil Shoham ◽  
Norman Metanis
Keyword(s):  
Protein Structure ◽  
Protein Stability ◽  
Disulfide Bond ◽  
Trypsin Inhibitor ◽  
Biological Function ◽  
Bovine Pancreatic Trypsin Inhibitor ◽  
Folding Mechanism ◽  
Pancreatic Trypsin Inhibitor ◽  
Model Protein

The folding mechanism of the model protein bovine pancreatic trypsin inhibitor was revisited. By switching the solvent exposed disulfide bond with methylene thioacetal we uncovered a hidden pathway in its folding mechanism. In addition, this moiety enhanced protein stability while fully maintaining the protein structure and biological function.

The influence of putrescine on the structure, enzyme activity and stability of α-chymotrypsin

RSC Advances ◽  
2016 ◽  
Vol 6 (35) ◽  
pp. 29264-29278 ◽  
Author(s):  
Sadegh Farhadian ◽  
Behzad Shareghi ◽  
Ali A. Saboury ◽  
Mina Evini
Keyword(s):  
Enzyme Activity ◽  
Protein Structure ◽  
Protein Stability ◽  
Structure Activity

Information on protein stability is essential to study protein structure, activity, and interactions with ligands.

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