scholarly journals The ‘Relevant’ Stability of Proteins with Equilibrium Intermediates

2002 ◽  
Vol 2 ◽  
pp. 1209-1215 ◽  
Author(s):  
Javier Sancho ◽  
Marta Bueno ◽  
Luis A. Campos ◽  
Juan Fernandez-Recio ◽  
Maria Pilar Iran ◽  
...  
Keyword(s):  
Side Chain ◽  
Practical Issue ◽  
Single Chain ◽  
Native Conformation ◽  
Native State ◽  
Protein Activity ◽  
Overall Stability ◽  
Protein Stabilisation

Proteins perform many useful molecular tasks, and their biotechnological use continues to increase. As protein activity requires a stable native conformation, protein stabilisation is a major scientific and practical issue. Towards that end, many successful protein stabilisation strategies have been devised in recent years. In most cases, model proteins with a two-state folding equilibrium have been used to study and demonstrate protein stabilisation. Many proteins, however, display more complex folding equilibria where stable intermediates accumulate. Stabilising these proteins requires specifically stabilising the native state relative to the intermediates, as these are expected to lack activity. Here we discuss how to investigate the ‘relevant’ stability of proteins with equilibrium intermediates and propose a way to dissect the contribution of side chain interactions to the overall stability into the ‘relevant’ and ‘nonrelevant’ terms. Examples of this analysis performed on apoflavodoxin and in a single-chain mini antibody are presented.

scholarly journals An Epilepsy-Causing Mutation Leads to Co-Translational Misfolding

2020 ◽  
Author(s):  
Janire Urrutia ◽  
Alejandra Aguado ◽  
Carolina Gomis-Perez ◽  
Arantza Muguruza-Montero ◽  
Oscar R. Ballesteros ◽  
...  
Keyword(s):  
Structural Instability ◽  
Side Chain ◽  
Binding Assays ◽  
Native Conformation ◽  
Native State ◽  
Iq Motif ◽  
Epileptic Patients ◽  
Nascent Chain ◽  
Inherited Mutations

AbstractProtein folding to the native state is particularly relevant in human diseases where inherited mutations lead to structural instability, aggregation and degradation. In general, the amino acid sequence carries all the necessary information for the native conformation, but the vectorial nature of translation can determine the folding outcome. Calmodulin (CaM) recognizes the properly folded Calcium Responsive Domain (CRD) of Kv7.2 channels. Within the IQ motif (helix A), the W344R mutation found in epileptic patients has negligible consequences for the structure of the complex as monitored by multiple in vitro binding assays and molecular dynamic computations. In silico studies revealed two orientations of the side chain, which are differentially populated by WT and W344R variants. Binding to CaM is impaired when the mutated protein is produced in cellulo but not in vitro, suggesting that this mutation impedes proper folding during translation within the cell by forcing the nascent chain to follow a folding route that leads to a non-native configuration, and thereby generating non-functional ion channels that fail to traffic to proper neuronal compartments.

scholarly journals Quaternized Amphiphilic Block Copolymers as Antimicrobial Agents

Polymers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 250
Author(s):  
Chih-Hao Chang ◽  
Chih-Hung Chang ◽  
Ya-Wen Yang ◽  
Hsuan-Yu Chen ◽  
Shu-Jyuan Yang ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Growth Efficiency ◽  
Amphiphilic Block Copolymers ◽  
Bacterial Growth Efficiency ◽  
Side Chain ◽  
Single Chain ◽  
Polymer Morphology ◽  
Hemolytic Effect ◽  
Solvent Environment ◽  
Controllable Factor

In this study, a novel polystyrene-block-quaternized polyisoprene amphipathic block copolymer (PS-b-PIN) is derived from anionic polymerization. Quaternized polymers are prepared through post-quaternization on a functionalized polymer side chain. Moreover, the antibacterial activity of quaternized polymers without red blood cell (RBCs) hemolysis can be controlled by block composition, side chain length, and polymer morphology. The solvent environment is highly related to the polymer morphology, forming micelles or other structures. The polymersome formation would decrease the hemolysis and increase the electron density or quaternized groups density as previous research and our experiment revealed. Herein, the PS-b-PIN with N,N-dimethyldodecylamine as side chain would form a polymersome structure in the aqueous solution to display the best inhibiting bacterial growth efficiency without hemolytic effect. Therefore, the different single-chain quaternized groups play an important role in the antibacterial action, and act as a controllable factor.

scholarly journals TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions

2017 ◽  
Author(s):  
Vinícius G. Contessoto ◽  
Vinícius M. de Oliveira ◽  
Bruno R. Fernandes ◽  
Gabriel G. Slade ◽  
Vitor B. P. Leite
Keyword(s):  
Web Server ◽  
Side Chain ◽  
Positive Energy ◽  
State University ◽  
Native State ◽  
Protein Charge ◽  
The Monte Carlo Method ◽  
Free Energy Contribution ◽  
Thermal Stability Of ◽  
Charge Interactions

AbstractThe TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to protein native state stability. The server also indicates which residues contribute to destabilizing the protein native state with positive energy and the side chain exposed to solvent. This residue is a candidate for mutation to increase protein thermostability as a function of the chosen pH condition. The web server is freely available at UNESP (São Paulo State University - DF/IBILCE): http://tksamc.df.ibilce.unesp.br.

EXPLORING THE ROLE OF C–H … π INTERACTIONS ON THE STRUCTURAL STABILITY OF ANTIMICROBIAL PEPTIDES

2009 ◽  
Vol 08 (05) ◽  
pp. 909-924 ◽  
Author(s):  
K. RAMANATHAN ◽  
RAO SETHUMADHAVAN
Keyword(s):  
Antimicrobial Peptides ◽  
Computational Analysis ◽  
Solvent Accessibility ◽  
Side Chain ◽  
Data Set ◽  
Π Interactions ◽  
Predominant Type ◽  
Overall Stability ◽  
Charmm Force Field

A computational analysis on the C – H … π interactions in a group of 53 antimicrobial peptides was investigated. A total of 162 C – H … π interactions were observed. Side-chain to side-chain C – H … π interactions are the predominant type of interactions in antimicrobial peptides data set. There was an average of one significant C – H … π interaction for every 7 residues in the antimicrobial peptides investigated. Long-range C – H … π interactions are the predominant type of interactions. The secondary structure preference, solvent accessibility and stabilization centers of these of C – H … π interacting residues were estimated. It is likely that the C – H … π interactions contribute significantly to the overall stability of antimicrobial peptides. These interactions were observed after a molecular dynamics study on these set of antimicrobial peptides using CHARMM force field.

scholarly journals Reversible deactivation of β-lactamase by quinacillin. Extent of the conformational change in the isolated transitory complex

1986 ◽  
Vol 237 (3) ◽  
pp. 723-730 ◽  
Author(s):  
K C Persaud ◽  
R H Pain ◽  
R Virden
Keyword(s):  
Relative Viscosity ◽  
Fold Increase ◽  
Order Rate Constant ◽  
Side Chain ◽  
Native State ◽  
Significant Difference ◽  
Unfolded State ◽  
Normal Enzyme ◽  
Partially Unfolded ◽  
Asymmetric Environment

Conditions have been established where the deactivation of the beta-lactamase from Staphylococcus aureus PC1 by the penicillin substrate, quinacillin, is close to complete but fully reversible. The temperature-dependence of the rate of re-activation indicated a half-life of about 170 min for the deactivated state at 0 degrees C. Measurement of the relative viscosity of mixtures of enzyme and quinacillin at 8.4 degrees C ruled out any significant difference in shape or solvation between the deactivated and the normal enzyme. C.d. measurements of the deactivated protein, separated from excess quinacillin, showed that the quinacillin side-chain chromophore was bound in an asymmetric environment. The ellipticity associated with the bound quinacillin chromophore decreased with the same first-order rate constant as that for reappearance of enzyme activity. These findings support the accumulation of a deactivated state that contains bound quinacillin or a derivative. Quinacillin caused a 3-fold increase in the rate of 3H exchange-out (at a rate that was low compared with that for the substantially unfolded or expanded protein). However, there was rapid exchange-out of about 50 3H atoms on addition of 1 M-urea to the deactivated enzyme, whereas the same concentration had no effect on the exchange-out of 3H from native enzyme. The interpretation that quinacillin increases the susceptibility of the native state to unfolding in the presence of urea is supported by the demonstration that SO4(2)- ions decreased the rate and extent of deactivation but had no effect on the rate of re-activation, as predicted from the observation that SO4(2)- ions, in competition with urea, stabilize the native state relative to the partially unfolded state H [Mitchinson & Pain (1985) J. Mol. Biol. 184, 331-342].

scholarly journals Forced unfolding of protein-inspired single-chain random heteropolymers

2021 ◽  
Author(s):  
Zexiang Han ◽  
Shayna Hilburg ◽  
Alfredo Alexander-Katz
Keyword(s):  
Protein Stabilization ◽  
Side Chain ◽  
Chemical Heterogeneity ◽  
Single Chain ◽  
High Chemical ◽  
Protection Mechanism ◽  
Sequence Composition ◽  
Nanoscale Mechanics ◽  
Topological Design ◽  
Dynamics Simulations

Synthetic random heteropolymers (RHPs) with high chemical heterogeneity can self-assemble into single-chain nanoparticles that exhibit features reminiscent of natural proteins, such as topological polymorphism. Using all-atom molecular dynamics simulations, this work investigates the structure and single-chain mechanical unfolding of a library of four-component RHPs in water, studying the effects of sequence, composition, configuration, and molecular weight. Results show that compactified RHPs can have highly dynamic unfolding behaviors which are dominated by complex side-chain interactions and prove markedly different from their homopolymer counterparts. For a given sequence and conformation, an RHP’s backbone topology can strongly impact its unfolding response, hinting at the importance of topological design in the nanoscale mechanics of heteropolymers. In addition, we identify enthalpically-driven reconfiguration upon unfolding, observing a solvent-shielding protection mechanism similar to protein stabilization by PEGylation. This work provides the first computational evidence for the force-induced unfolding of protein-inspired multicomponent heteropolymers.

scholarly journals Does protein A mirror image exist in solution? Outline of an experimental design aimed to detect it

2018 ◽  
Author(s):  
Osvaldo A. Martin ◽  
Yury Vorobjev ◽  
Harold A. Scheraga ◽  
Jorge A. Vila
Keyword(s):  
Experimental Design ◽  
Protein A ◽  
Mirror Image ◽  
Direct Application ◽  
Computational Simulations ◽  
Native Conformation ◽  
Native State ◽  
Theoretical Evidence ◽  
Image State ◽  
Unsolved Issue

ABSTRACTThere is abundant theoretical evidence indicating that a mirror image of ProteinA may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on computational simulations indicating that the use of a mutant of protein A, namely 01 OH, could be used to detect the mirror image conformation in solution. Our results indicate that the native conformation of the protein A should have a pKa, for the 01 OH mutant, at r06.2, while the mirror image conformation should have a pKa close to ≈7.3. Naturally, if all the population is in the native state for the 01 OH mutant, the pKa should be ≈6.2, while, if all are in the mirror image state, it would be ≈7.3, and, if it is a mixture, the pKa should be larger than 6.2, presumably in proportion to the mirror population. In addition, evidence is provided indicating the tautomeric distribution of H1O must also change between the native and mirror conformations. Although this may not be completely relevant for the purpose of determining whether the protein A mirror image exists in solution, it could provide valuable information to validate the pKa findings. We hope this proposal will foster experimental work on this problem either by direct application of our proposed experimental design or serving as inspiration and motivation for other experiments.

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