Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the α-helix fragment

1997 ◽  
Vol 2 (2) ◽  
pp. 123-133 ◽  
Author(s):  
Francisco J Blanco ◽  
Angel R Ortiz ◽  
Luis Serrano
Keyword(s):  
Conformational Analysis ◽  
Protein G ◽  
B1 Domain ◽  
Α Helix

scholarly journals The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G

2018 ◽  
Vol 18 (1) ◽  
pp. 186
Author(s):  
Tony Ibnu Sumaryada ◽  
Kania Nur Sawitri ◽  
Setyanto Tri Wahyudi
Keyword(s):  
Tertiary Structure ◽  
Salt Bridge ◽  
Protein G ◽  
Core Collapse ◽  
Hydrophobic Core ◽  
B1 Domain ◽  
Collapse Model ◽  
Α Helix ◽  
Dynamics Simulations

Molecular dynamics simulations of the B1 fragment of protein G (56 residues) have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance) of the salt-bridge pairs E27–K31 (in the α-helix) and E56–K10 (connecting β4 and β1) has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained

scholarly journals Mechanics and dynamics of B1 domain of protein G: Role of packing and surface hydrophobic residues

2008 ◽  
Vol 8 (1) ◽  
pp. 147-160 ◽  
Author(s):  
Marc A. Ceruso ◽  
Andrea Amadei ◽  
Alfredo Di Nola
Keyword(s):  
Protein G ◽  
Hydrophobic Residues ◽  
B1 Domain

Role of the amino acid sequence in domain swapping of the B1 domain of protein G

2008 ◽  
Vol 72 (1) ◽  
pp. 88-104 ◽  
Author(s):  
Fernanda L. Sirota ◽  
Stephanie Héry-Huynh ◽  
Sebastian Maurer-Stroh ◽  
Shoshana J. Wodak
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Domain Swapping ◽  
Protein G ◽  
B1 Domain

scholarly journals Structural and Technological Approach to Reveal the Role of the Lipid Phase in the Formation of Soy Emulsion Gels with Chia Oil

Gels ◽  
2021 ◽  
Vol 7 (2) ◽  
pp. 48
Author(s):  
Ana M. Herrero ◽  
Claudia Ruiz-Capillas
Keyword(s):  
Raman Spectroscopy ◽  
Structural Properties ◽  
Structural Changes ◽  
Protein Secondary Structure ◽  
Lipid Phase ◽  
Α Helix ◽  
Β Sheet ◽  
Shed Light ◽  
Chia Oil

Considerable attention has been paid to emulsion gels (EGs) in recent years due to their interesting applications in food. The aim of this work is to shed light on the role played by chia oil in the technological and structural properties of EGs made from soy protein isolates (SPI) and alginate. Two systems were studied: oil-free SPI gels (SPI/G) and the corresponding SPI EGs (SPI/EG) that contain chia oil. The proximate composition, technological properties (syneresis, pH, color and texture) and structural properties using Raman spectroscopy were determined for SPI/G and SPI/EG. No noticeable (p > 0.05) syneresis was observed in either sample. The pH values were similar (p > 0.05) for SPI/G and SPI/EG, but their texture and color differed significantly depending on the presence of chia oil. SPI/EG featured significantly lower redness and more lightness and yellowness and exhibited greater puncture and gel strengths than SPI/G. Raman spectroscopy revealed significant changes in the protein secondary structure, i.e., higher (p < 0.05) α-helix and lower (p < 0.05) β-sheet, turn and unordered structures, after the incorporation of chia oil to form the corresponding SPI/EG. Apparently, there is a correlation between these structural changes and the textural modifications observed.

scholarly journals Conformational Analysis of CmH2m+1OCH2CH2OH (m = 1-4): The Role of CH.cntdot..cntdot..cntdot.O Intramolecular Interactions

1995 ◽  
Vol 99 (20) ◽  
pp. 8066-8070 ◽  
Author(s):  
Francisco P. S. C. Gil ◽  
A. M. Amorim Da Costa ◽  
J. J. C. Teixeira-Dias
Keyword(s):  
Conformational Analysis ◽  
Intramolecular Interactions

scholarly journals Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes

2006 ◽  
Vol 103 (32) ◽  
pp. 11904-11909 ◽  
Author(s):  
P. Selenko ◽  
Z. Serber ◽  
B. Gadea ◽  
J. Ruderman ◽  
G. Wagner
Keyword(s):  
Xenopus Laevis ◽  
Protein G ◽  
Nmr Analysis ◽  
Quantitative Nmr ◽  
B1 Domain ◽  
Egg Extracts

scholarly journals The role of context on α-helix stabilization: Host-guest analysis in a mixed background peptide model

1997 ◽  
Vol 6 (6) ◽  
pp. 1264-1272 ◽  
Author(s):  
Jianxin Yang ◽  
Erik J. Spek ◽  
Youxiang Gong ◽  
Hongxing Zhou ◽  
Neville R. Kallenbach
Keyword(s):  
Α Helix

scholarly journals TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Marc Perea ◽  
Ivar Lugtenburg ◽  
Eduardo Mayol ◽  
Arnau Cordomí ◽  
Xavier Deupí ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Sequence Motifs ◽  
Web Servers ◽  
Structural Role ◽  
Α Helix

Cationicity and hydrophobicity enhance the cytotoxic potency of Phoratoxin C anticancer peptide analogues against triple negative breast cancer cells

2021 ◽  
Vol 17 ◽  
Author(s):  
Chu Xin Ng ◽  
Cheng Foh Le ◽  
Sau Har Lee
Keyword(s):  
Cancer Cells ◽  
Anticancer Agents ◽  
Breast Cancer Cells ◽  
Critical Role ◽  
Three Dimensional ◽  
Vero Cells ◽  
Anticancer Peptides ◽  
Α Helix ◽  
Peptide Analogues

Background: Anticancer peptides (ACPs) have received increasing attention as a promising class of novel anticancer agents owing to its potent and rapid cytotoxic properties. In this study, we aim to investigate the effects of cationicity and hydrophobicity in modulating the cytotoxicity of PtxC, a class of ACP from the leafy mistletoe Phoradendron tomentosum against the MDA-MB-231 and Vero cells. Method: We designed a series of four PtxC analogues (PA1 – PA4) by residual substitutions with specific amino acids to introduce the specific charge and hydrophobicity alterations to the analogues. The cytotoxicity strength of the PtxC analogues on MDA-MB-231 and Vero cells were tested by using MTT assay at 24 hours post treatment. Results: PA1, PA2 and PA4 displayed marked increases in cytotoxicity against both MDA-MB-231 and Vero cells and can be ranked in the order of PA2 > PA4 > PA1 > PtxC > PA3. Sequence-activity relationship analyses of the designed analogues showed that an increase in the level of cationicity and hydrophobicity correlated well with the enhanced cytotoxic activity of PtxC analogues. This was observed with PA1 (netC +8) and PA2 (netC +10) in comparison to PtxC (netC +7). Similar finding was observed for PA4 (GRAVY +0.070) in contrast to PtxC (GRAVY -0.339). Three-dimensional modelling predicted a double α-helix structure in PtxC class of ACP. The larger first helix in PA2 and PA4 was suggested to be responsible for the enhanced cytotoxicity observed. Conclusion: The critical role of cationicity and hydrophobicity in enhancing cytotoxicity of PtxC class of ACPs were clearly demonstrated in our study. The current findings could be extrapolated to benefit peptide design strategy in other classes of ACPs toward the discovery of highly potent ACPs against cancer cells as potential novel therapeutic agents.

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