Intermediates Stabilized by Tryptophan Pairs Exist in Trpzip Beta-Hairpins

Biochemistry ◽  
2014 ◽  
Vol 53 (38) ◽  
pp. 5978-5986 ◽  
Author(s):  
Zhongbo Yu ◽  
Sangeetha Selvam ◽  
Hanbin Mao
Keyword(s):  
Beta Hairpins

scholarly journals Four classes of β-hairpins in proteins

1986 ◽  
Vol 240 (1) ◽  
pp. 289-292 ◽  
Author(s):  
E J Milner-White ◽  
R Poet
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Frequency Of Occurrence ◽  
Single Class ◽  
Three Dimensional Structure ◽  
Beta Hairpins ◽  
Beta Hairpin

We show that beta-hairpins can be divided into four classes, each with a number of members. Hairpins from a single class are readily interconverted by loss or gain of hydrogen bonds, but interconversion between classes requires complete unzipping and reformation of the entire beta-hairpin. Sibanda & Thornton [(1985) Nature (London) 316, 170-174] have classified beta-hairpins as either two-residue, three-residue, four-residue etc., loops. We point out that their nomenclature, by itself, gives rise to ambiguities, but that, if the class (one of the four mentioned above) is also specified, the description of beta-hairpins becomes straightforward. A range of proteins of known three-dimensional structure has been examined; it provides examples of hairpins of each of the four classes and give some indication of their frequency of occurrence. The distribution observed is substantially different from that described by Sibanda & Thornton [(1985) Nature (London) 316, 170-174].

Structural and sequence features of two residue turns in beta-hairpins

2014 ◽  
Vol 82 (9) ◽  
pp. 1721-1733 ◽  
Author(s):  
Bharat Madan ◽  
Sung Yong Seo ◽  
Sun-Gu Lee
Keyword(s):  
Sequence Features ◽  
Beta Hairpins

scholarly journals Beta-hairpins in proteins revisited: lessons for de novo design

1997 ◽  
Vol 10 (10) ◽  
pp. 1131-1141 ◽  
Author(s):  
K. Gunasekaran ◽  
C. Ramakrishnan ◽  
P. Balaram
Keyword(s):  
De Novo ◽  
De Novo Design ◽  
Beta Hairpins

scholarly journals Modeling the Mechanism of CLN025 Beta-Hairpin Formation

2017 ◽  
Author(s):  
Keri A. McKiernan ◽  
Brooke E. Husic ◽  
Vijay S. Pande
Keyword(s):  
Force Fields ◽  
Test Case ◽  
Conformational Ensemble ◽  
Folding Process ◽  
Hydrophobic Collapse ◽  
Rate Determining Step ◽  
Beta Hairpins ◽  
Beta Hairpin ◽  
State Models ◽  
Protein Force Fields

Beta-hairpins are a substructure found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

scholarly journals Effects of Claudin-1 on the Action of Clostridium perfringens Enterotoxin in Caco-2 Cells

Toxins ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 582
Author(s):  
Mehdizadeh Gohari ◽  
Li ◽  
Navarro ◽  
Uzal ◽  
McClane
Keyword(s):  
Complex Formation ◽  
Clostridium Perfringens ◽  
Paracellular Permeability ◽  
Null Mutant ◽  
Wild Type ◽  
Clostridium Perfringens Enterotoxin ◽  
Beta Barrel ◽  
Small Complex ◽  
Beta Hairpins ◽  
Increased Sensitivity

Clostridium perfringens enterotoxin (CPE) contributes to diarrhea and an often-lethal enterotoxemia. CPE action starts when it binds to claudin receptors, forming a small complex (90 kDa). Six small complexes then oligomerize to create prepores, followed by insertion of beta-hairpins from CPE to form beta-barrel pores named CH-1 or CH-2. Of the ~27 members of the human claudin protein family, only some bind CPE. However, both receptor claudins and the nonreceptor claudin-1 (CLDN-1) are associated with the small and CH-1/CH-2 CPE complexes. Therefore, this study evaluated whether claudin-1 affects CPE action by generating a CLDN-1 null mutant in Caco-2 cells using CRISPR-Cas9. Compared to wild-type Caco-2 cells, paracellular permeability of the CLDN-1 mutant was significantly enhanced, suggesting that claudin-1 may reduce CPE absorption during enterotoxemia. The CLDN-1 mutant was also markedly more sensitive than wild-type Caco-2 cells to apically-applied CPE. The mechanism behind this increased sensitivity involved higher CPE binding by the CLDN-1 mutant vs. wild-type Caco-2 cells, which led to more CH-1/CH-2 complex formation. However, the CH-1/CH-2 complexes formed by the CLDN-1 mutant were less stable or trypsin resistant than those of wild-type cells. These results indicate that, although a nonreceptor, CLDN-1 positively and negatively influences CPE action.

scholarly journals Using Hydrogen Bond Surrogate Technology to Stabilize Beta-Hairpins

2017 ◽  
Vol 112 (3) ◽  
pp. 177a
Author(s):  
Nicholas Sawyer ◽  
Paramjit S. Arora
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bond Surrogate ◽  
Beta Hairpins

scholarly journals Hydrogen Bond Surrogate Beta-Hairpins to Inhibit Protein-Protein Interactions

2018 ◽  
Vol 114 (3) ◽  
pp. 56a-57a
Author(s):  
Nicholas Sawyer ◽  
Paramjit S. Arora
Keyword(s):  
Hydrogen Bond ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Hydrogen Bond Surrogate ◽  
Beta Hairpins

scholarly journals Understanding how Beta-Hairpins Fold using Molecular Dynamics Simulations in Multiple Force Fields

2018 ◽  
Vol 114 (3) ◽  
pp. 208a-209a
Author(s):  
Brooke E. Husic ◽  
Keri A. McKiernan ◽  
Vijay S. Pande
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Beta Hairpins ◽  
Dynamics Simulations
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