Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

2004 ◽  
Vol 121 (5) ◽  
pp. 2412-2421 ◽  
Author(s):  
Edward Z. Wen ◽  
Ray Luo
Keyword(s):  
Secondary Structures ◽  
Side Chain ◽  
Denatured State

scholarly journals Role of Side Chain Size in the Formation of Secondary Structures in Model Peptides

2015 ◽  
Vol 108 (2) ◽  
pp. 519a
Author(s):  
Farbod Mahmoudinobar ◽  
Cristiano L. Dias ◽  
Ronen Zangi
Keyword(s):  
Secondary Structures ◽  
Side Chain ◽  
Model Peptides

scholarly journals Tying up the Loose Ends: A Mathematically Knotted Protein

2021 ◽  
Vol 9 ◽  
Author(s):  
Shang-Te Danny Hsu ◽  
Yun-Tzai Cloud Lee ◽  
Kornelia M. Mikula ◽  
Sofia M. Backlund ◽  
Igor Tascón ◽  
...  
Keyword(s):  
Polymer Chains ◽  
Side Chain ◽  
Denatured State ◽  
Cofactor Binding ◽  
Physico Chemical ◽  
Theoretical Predictions ◽  
Backbone Cyclization ◽  
Knotted Protein ◽  
Chemical Attributes ◽  
Polypeptide Chains

Knots have attracted scientists in mathematics, physics, biology, and engineering. Long flexible thin strings easily knot and tangle as experienced in our daily life. Similarly, long polymer chains inevitably tend to get trapped into knots. Little is known about their formation or function in proteins despite >1,000 knotted proteins identified in nature. However, these protein knots are not mathematical knots with their backbone polypeptide chains because of their open termini, and the presence of a “knot” depends on the algorithm used to create path closure. Furthermore, it is generally not possible to control the topology of the unfolded states of proteins, therefore making it challenging to characterize functional and physicochemical properties of knotting in any polymer. Covalently linking the amino and carboxyl termini of the deeply trefoil-knotted YibK from Pseudomonas aeruginosa allowed us to create the truly backbone knotted protein by enzymatic peptide ligation. Moreover, we produced and investigated backbone cyclized YibK without any knotted structure. Thus, we could directly probe the effect of the backbone knot and the decrease in conformational entropy on protein folding. The backbone cyclization did not perturb the native structure and its cofactor binding affinity, but it substantially increased the thermal stability and reduced the aggregation propensity. The enhanced stability of a backbone knotted YibK could be mainly originated from an increased ruggedness of its free energy landscape and the destabilization of the denatured state by backbone cyclization with little contribution from a knot structure. Despite the heterogeneity in the side-chain compositions, the chemically unfolded cyclized YibK exhibited several macroscopic physico-chemical attributes that agree with theoretical predictions derived from polymer physics.

CuI-Catalyzed Azide–Alkyne Intramoleculari-to-(i+4) Side-Chain-to-Side-Chain Cyclization Promotes the Formation of Helix-Like Secondary Structures

2010 ◽  
Vol 2010 (3) ◽  
pp. 446-457 ◽  
Author(s):  
Mario Scrima ◽  
Alexandra Le Chevalier-Isaad ◽  
Paolo Rovero ◽  
Anna Maria Papini ◽  
Michael Chorev ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Side Chain

scholarly journals Twists or turns: stabilising alpha vs. beta turns in tetrapeptides

2019 ◽  
Vol 10 (45) ◽  
pp. 10595-10600
Author(s):  
Huy N. Hoang ◽  
Timothy A. Hill ◽  
Gloria Ruiz-Gómez ◽  
Frederik Diness ◽  
Jody M. Mason ◽  
...  
Keyword(s):  
Secondary Structures ◽  
Side Chain ◽  
Ring Size ◽  
Beta Turns

Twisting or turning peptides: ring size and chi angle in side chain cross-linked tetrapeptides together control α- or β-turn structures, which mimic irregular secondary structures in proteins.

scholarly journals 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content

2019 ◽  
Vol 47 (W1) ◽  
pp. W477-W481 ◽  
Author(s):  
Elliot D Drew ◽  
Robert W Janes
Keyword(s):  
Secondary Structure ◽  
Protein Structures ◽  
Secondary Structures ◽  
Residue Level ◽  
Side Chain ◽  
Related Protein ◽  
Tertiary Structures ◽  
Secondary Structure Content ◽  
Protein Secondary Structures

Abstract 2StrucCompare is a webserver whose primary aim is to visualize subtle but functionally important differences between two related protein structures, either of the same protein or related homologues, with similar or functionally different tertiary structures. At the heart of the package is identifying and visualizing differences between conformations at the secondary structure and at the residue level, such as contact differences or side chain conformational differences found between two protein chains. The protein secondary structures are determined according to four established methods (DSSP, STRIDE, P-SEA and STICKS), and as each employs different assignment strategies, small conformational differences between the two structures can give rise to paired residues being denoted as having different secondary structure features with the different methods. 2StrucCompare captures both the large and more subtle differences found between structures, enabling visualization of these differences that could be key to an understanding of a proteins’ function. 2StrucCompare is freely accessible at http://2struccompare.cryst.bbk.ac.uk/index.php

scholarly journals 1P-047 Roles of side-chain packing in the formation of secondary structures of a protein(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

2009 ◽  
Vol 49 (supplement) ◽  
pp. S70
Author(s):  
Satoshi Yasuda ◽  
Ryota Kodama ◽  
Takashi Yoshidome ◽  
Yuichi Harano ◽  
Masahiro Kinoshita
Keyword(s):  
Annual Meeting ◽  
Secondary Structures ◽  
Side Chain ◽  
Chain Packing ◽  
Biophysical Society ◽  
Side Chain Packing
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