scholarly journals A little walk from physical to biological complexity: protein folding and stability

2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Marianne Rooman
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Thermal Resistance ◽  
Protein Structures ◽  
Amino Acid Substitutions ◽  
Biological Complexity ◽  
Statistical Potentials ◽  
Bioinformatics Tools ◽  
The Stability ◽  
Boltzmann Law

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and the change of these quantities upon amino acid substitutions. These methods are based on knowledge-driven statistical potentials, derived from experimental protein structures using the inverse Boltzmann law.

scholarly journals Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

2021 ◽  
Vol 22 (17) ◽  
pp. 9653
Author(s):  
Jiacheng Li ◽  
Chengyu Hou ◽  
Xiaoliang Ma ◽  
Shuai Guo ◽  
Hongchi Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Amino Acid ◽  
Gibbs Free Energy ◽  
Energy Equation ◽  
Protein Structures ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrophobic Collapse ◽  
Polypeptide Chains

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

scholarly journals Study on the Influence of mRNA, the Genetic Language, on Protein Folding Rates

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruifang Li ◽  
Hong Li ◽  
Xue Feng ◽  
Ruifeng Zhao ◽  
Yongxia Cheng
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Protein Structures ◽  
Gc Content ◽  
Amino Acid Sequences ◽  
Information Redundancy ◽  
Folding Rate ◽  
Folding Rates ◽  
Related Information ◽  
Linear Regressions

Many works have reported that protein folding rates are influenced by the characteristics of amino acid sequences and protein structures. However, few reports on the problem of whether the corresponding mRNA sequences are related to the protein folding rates can be found. An mRNA sequence is regarded as a kind of genetic language, and its vocabulary and phraseology must provide influential information regarding the protein folding rate. In the present work, linear regressions on the parameters of the vocabulary and phraseology of mRNA sequences and the corresponding protein folding rates were analyzed. The results indicated that D2 (the adjacent base-related information redundancy) values and the GC content values of the corresponding mRNA sequences exhibit significant negative relations with the protein folding rates, but D1 (the single base information redundancy) values exhibit significant positive relations with the protein folding rates. In addition, the results show that the relationships between the parameters of the genetic language and the corresponding protein folding rates are obviously different for different protein groups. Some useful parameters that are related to protein folding rates were found. The results indicate that when predicting protein folding rates, the information from protein structures and their amino acid sequences is insufficient, and some information for regulating the protein folding rates must be derived from the mRNA sequences.

scholarly journals Additivity of the Stabilization Effect of Single Amino Acid Substitutions in Triple Mutants of Recombinant Formate Dehydrogenase from the Soybean Glycine max

Acta Naturae ◽  
2015 ◽  
Vol 7 (3) ◽  
pp. 55-64 ◽  
Author(s):  
A. A. Alekseeva ◽  
I. S. Kargov ◽  
S. Yu. Kleimenov ◽  
S. S. Savin ◽  
V I. Tishkov
Keyword(s):  
Thermal Stability ◽  
Glycine Max ◽  
Amino Acid ◽  
Formate Dehydrogenase ◽  
Single Amino Acid ◽  
Inactivation Kinetics ◽  
Amino Acid Substitutions ◽  
Stabilization Effect ◽  
The Stability ◽  
Thermal Stability Of

Recently, we demonstrated that the amino acid substitutions Ala267Met and Ala267Met/Ile272Val (Alekseeva et al., Biochemistry, 2012), Phe290Asp, Phe290Asn and Phe290Ser (Alekseeva et al., Prot. Eng. Des. Select, 2012) in recombinant formate dehydrogenase from soya Glycine max (SoyFDH) lead to a significant (up to 30-100 times) increase in the thermal stability of the enzyme. The substitutions Phe290Asp, Phe290Asn and Phe290Ser were introduced into double mutant SoyFDH Ala267Met/Ile272Val by site-directed mutagenesis. Combinations of three substitutions did not lead to a noticeable change in the catalytic properties of the mutant enzymes. The stability of the resultant triple mutants was studied through thermal inactivation kinetics and differential scanning calorimetry. The thermal stability of the new mutant SoyFDHs was shown to be much higher than that of their precursors. The stability of the best mutant SoyFDH Ala267Met/Ile272Val/Phe290Asp turned out to be comparable to that of the most stable wild-type formate dehydrogenases from other sources. The results obtained with both methods indicate a great synergistic contribution of individual amino acid substitutions to the common stabilization effect.

scholarly journals Multiple substitutions lead to increased loop flexibility and expanded specificity in Acinetobacter baumannii carbapenemase OXA-239

2018 ◽  
Vol 475 (1) ◽  
pp. 273-288 ◽  
Author(s):  
Thomas M. Harper ◽  
Cynthia M. June ◽  
Magdalena A. Taracila ◽  
Robert A. Bonomo ◽  
Rachel A. Powers ◽  
...  
Keyword(s):  
Amino Acid ◽  
Acinetobacter Baumannii ◽  
Active Site ◽  
Active Sites ◽  
Protein Structures ◽  
Amino Acid Substitutions ◽  
The Third ◽  
Class D ◽  
Late Generation ◽  
Loop Flexibility

OXA-239 is a class D carbapenemase isolated from an Acinetobacter baumannii strain found in Mexico. This enzyme is a variant of OXA-23 with three amino acid substitutions in or near the active site. These substitutions cause OXA-239 to hydrolyze late-generation cephalosporins and the monobactam aztreonam with greater efficiency than OXA-23. OXA-239 activity against the carbapenems doripenem and imipenem is reduced ∼3-fold and 20-fold, respectively. Further analysis demonstrated that two of the substitutions (P225S and D222N) are largely responsible for the observed alteration of kinetic parameters, while the third (S109L) may serve to stabilize the protein. Structures of OXA-239 with cefotaxime, doripenem and imipenem bound as acyl-intermediates were determined. These structures reveal that OXA-239 has increased flexibility in a loop that contains P225S and D222N. When carbapenems are bound, the conformation of this loop is essentially identical with that observed previously for OXA-23, with a narrow active site that makes extensive contacts to the ligand. When cefotaxime is bound, the loop can adopt a different conformation that widens the active site to allow binding of that bulky drug. This alternate conformation is made possible by P225S and further stabilized by D222N. Taken together, these results suggest that the three substitutions were selected to expand the substrate specificity profile of OXA-23 to cephalosporins and monobactams. The loss of activity against imipenem, however, suggests that there may be limits to the plasticity of class D enzymes with regard to evolving active sites that can effectively bind multiple classes of β-lactam drugs.

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