Importance of Two Buried Salt Bridges in the Stability and Folding Pathway of Barnase†

Biochemistry ◽  
1996 ◽  
Vol 35 (21) ◽  
pp. 6786-6794 ◽  
Author(s):  
A. C. Tissot ◽  
S. Vuilleumier ◽  
A. R. Fersht
Keyword(s):  
Folding Pathway ◽  
Salt Bridges ◽  
The Stability

Two- and four-armed hetero porphyrin dimers: Influence of the number of arms on the stability and specific recognition behaviour

2021 ◽  
Author(s):  
Masaki Ueda ◽  
Masaki Kimura ◽  
Shinobu Miyagawa ◽  
Masaya Naito ◽  
Hikaru Takaya ◽  
...  
Keyword(s):  
Salt Bridges ◽  
Specific Recognition ◽  
Self Assembled ◽  
The Stability ◽  
Porphyrin Dimers

In this study we self-assembled the four-armed porphyrin hetero dimer capsule Cap4, stabilized through amidinium–carboxylate salt bridges, in CH2Cl2 and CHCl3. The dimer capsule Cap4 was kinetically and thermodynamically more...

scholarly journals Context-dependent effects of proline residues on the stability and folding pathway of ubiquitin

2004 ◽  
Vol 271 (22) ◽  
pp. 4474-4484 ◽  
Author(s):  
Maria D. Crespo ◽  
Geoffrey W. Platt ◽  
Roger Bofill ◽  
Mark S. Searle
Keyword(s):  
Folding Pathway ◽  
Context Dependent ◽  
The Stability

Effects of engineered salt bridges on the stability of subtilisin BPN'

1990 ◽  
Vol 4 (1) ◽  
pp. 87-97 ◽  
Author(s):  
C.R. Erwin ◽  
B.L. Barnett ◽  
J.D. Oliver ◽  
J.F. Sullivan
Keyword(s):  
Salt Bridges ◽  
The Stability

scholarly journals Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvationThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 371-381 ◽  
Author(s):  
Will C. Guest ◽  
Neil R. Cashman ◽  
Steven S. Plotkin
Keyword(s):  
Prion Protein ◽  
Electrostatic Potential ◽  
Peer Review Process ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Self Energy ◽  
Low Dielectric ◽  
The Stability ◽  
Α Helix ◽  
Electrostatic Potential Energy

Using a recently developed mesoscopic theory of protein dielectrics, we have calculated the salt bridge energies, total residue electrostatic potential energies, and transfer energies into a low dielectric amyloid-like phase for 12 species and mutants of the prion protein. Salt bridges and self energies play key roles in stabilizing secondary and tertiary structural elements of the prion protein. The total electrostatic potential energy of each residue was found to be invariably stabilizing. Residues frequently found to be mutated in familial prion disease were among those with the largest electrostatic energies. The large barrier to charged group desolvation imposes regional constraints on involvement of the prion protein in an amyloid aggregate, resulting in an electrostatic amyloid recruitment profile that favours regions of sequence between α helix 1 and β strand 2, the middles of helices 2 and 3, and the region N-terminal to α helix 1. We found that the stabilization due to salt bridges is minimal among the proteins studied for disease-susceptible human mutants of prion protein.

scholarly journals How well do force fields capture the strength of salt bridges in proteins?

2018 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Enhanced Sampling ◽  
Important Interaction ◽  
Close Proximity ◽  
The Stability ◽  
Dynamics Simulations

AbstractSalt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulations is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depend on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is slightly overestimated in simulations of GB1 using six commonly used combinations of force fields and water models. We therefore conclude that further work is needed to refine our ability to model quantitatively the stability of salt bridges through simulations, and that comparisons between experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

Investigation on salt bridge interactions of mammalian prion proteins by molecular dynamics simulation / Memeli prion proteinlerinin moleküler dinamik simulasyon ile tuz köprüleri etkileşimlerinin araştırılması

2016 ◽  
Vol 41 (3) ◽  
Author(s):  
Xiliang Chen ◽  
Xin Chen ◽  
Yafang Liu
Keyword(s):  
Molecular Dynamics ◽  
Prion Protein ◽  
Electrostatic Interactions ◽  
Prion Proteins ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Salt Bridges ◽  
Tertiary Structures ◽  
Local Structures ◽  
The Stability

AbstractObjective: Salt bridge interaction is one of the most important electrostatic interactions to stabilize the secondary and tertiary structures of protein. To obtain more insight into the molecular basis of prion proteins, the salt bridge networks in two animal prion proteins are studied in this work.Methods: Molecular dynamics (MD) and Flow MD (FMD) simulations are employed to investigate the salt bridges interactions of rabbit prion protein (rPrPc), Syrian hamster prion protein (syPrPc) and the variants of the two prion proteins.Results: The dynamic behaviors of salt bridges are characterized, and the relation between salt bridge interactions and local structures are also discussed. The type of salt bridges in the two prion proteins is divided into the helixloop, intra-helix and inter-helix salt bridges. It is found that the helix-loop salt bridges is more important for the stability of prion proteins than the other two kinds of slat bridge.Conclusion: The Asp201-Arg155 (rS1), Asp177-Arg163 (rS3) and Asp178-Arg164 (syS1) are the important salt bridges to stabilize the structures of rPrPc and syPrPc, respectively. The structural stability is partly depended on the number of helix-loop salt bridge.

The relevance of salt bridges for the stability of the influenza virus hemagglutinin

2007 ◽  
Vol 21 (4) ◽  
pp. 995-1002 ◽  
Author(s):  
P. Sivaramakrishna Rachakonda ◽  
Michael Veit ◽  
Thomas Korte ◽  
Kai Ludwig ◽  
Christoph Böttcher ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Salt Bridges ◽  
Influenza Virus Hemagglutinin ◽  
The Stability

Insights into stabilizing interactions in the distorted domain-swapped dimer ofSalmonella typhimuriumsurvival protein

2015 ◽  
Vol 71 (9) ◽  
pp. 1812-1823 ◽  
Author(s):  
Yamuna Kalyani Mathiharan ◽  
H. S. Savithri ◽  
M. R. N. Murthy
Keyword(s):  
Hydrogen Bond ◽  
Catalytic Activity ◽  
Salt Bridge ◽  
Salt Bridges ◽  
X Ray ◽  
Dimeric Interface ◽  
Distorted Structure ◽  
Dimeric Protein ◽  
The Stability

The survival protein SurE fromSalmonella typhimurium(StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of β-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167°. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11° between theBchains upon superposition of theAchains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.

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