Design of Stable α-Helical Peptides and Thermostable Proteins in Biotechnology and Biomedicine

Yakimov, Alexander; Afanaseva, A S; Khodorkovskiy, Mikhail; Petukhov, Michael

doi:10.32607/20758251-2016-8-4-70-81

Cited by 36 publications

(25 citation statements)

References 113 publications

(147 reference statements)

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“…The helical stability of the peptides was studied by molecular dynamics using two different membrane models, E. coli and S. aureus, in order to understand the antibacterial selectivity that emerges after the replacement of the residues. It is well known that the most frequent secondary structure in AMPs is the α-helix, given the importance of its interactions with other proteins, nucleic acids, and lipids of cell membranes [34,35]. In fact, the type of phospholipid modulates the interactions with the peptide, having an impact on the stability of its structure and therefore on its activity [36].…”

Section: Discussionmentioning

confidence: 99%

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

et al. 2019

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Recently, resistance of pathogens towards conventional antibiotics has increased, representing a threat to public health globally. As part of the fight against this, studies on alternative antibiotics such as antimicrobial peptides have been performed, and it has been shown that their sequence and structure are closely related to their antimicrobial activity. Against this background, we here evaluated the antibacterial activity of two peptides developed by solid-phase synthesis, Alyteserin 1c (WT) and its mutant derivative (ΔM), which shows increased net charge and reduced hydrophobicity. These structural characteristics were modified as a result of amino acid substitutions on the polar face of the WT helix. The minimum inhibitory concentration (MIC) of both peptides was obtained in Gram-positive and Gram-negative bacteria. The results showed that the rational substitutions of the amino acids increased the activity in Gram-positive bacteria, especially against Staphylococcus aureus, for which the MIC was one-third of that for the WT analog. In contrast to the case for Gram-positive bacteria, these substitutions decreased activity against Gram-negative bacteria, especially in Escherichia coli, for which the MIC was eight-fold higher than that exhibited by the WT peptide. To understand this, models of the peptide behavior upon interacting with membranes of E. coli and S. aureus created using molecular dynamics were studied and it was determined that the helical stability of the peptide is indispensable for antimicrobial activity. The hydrogen bonds between the His20 of the peptides and the phospholipids of the membranes should modulate the selectivity associated with structural stability at the carboxy-terminal region of the peptides.

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Section: Discussionmentioning

confidence: 99%

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

et al. 2019

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“…Molecular structure visualization, analysis and protein sequence alignment was carried out using the Molsoft ICM Pro software package ( 25 ). Peptides were designed using SEQOPT software for global sequence optimization to maximize α-helix stabilizing interactions of peptide (available on http://mml.spbstu.ru/seqopt/ ) ( 22 – 24 ). The SEQOPT method generates amino acid sequences with the maximum possible conformational stability at any given environmental conditions (temperature, pH and ionic strength) and arbitrary set of fixed amino acids if they are necessary for the functional activity of the peptide.…”

Section: Methodsmentioning

confidence: 99%

“…Recently we have developed a method (SEQOPT) for the design of α-helices of maximum stability in short monomeric peptides ( 22 – 24 ) using global sequence optimization. Unlike other approaches used to increase conformational stability of protein α-helices by adding a few stabilizing interactions to the protein structure, this method deals with all possible sequences of 20 natural amino acids and selects the best one from them.…”

Section: Introductionmentioning

confidence: 99%

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide

Yakimov

Pobegalov

Bakhlanova

et al. 2017

Nucleic Acids Research

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The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.

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“…Forming an α‐helical structure can stabilize a peptide, and rational design can be used to improve the propensity to form α‐helices and the stability of the helices. Using rational design, α‐helicity can be engineered via intramolecular salt bridges using Glu, Asp, Arg, or Lys salt bridges to increase helicity .…”

Section: Protein Engineering To Design Peptide Characteristicsmentioning

confidence: 99%

Beyond function: Engineering improved peptides for therapeutic applications

2019

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Peptides are a promising source of new therapeutics, but the biophysical characteristics of natural peptides, including their stability and propensity to aggregate, can limit their success. Protein engineering offers powerful tools to improve the properties of peptides for biological applications. In this review, we explain rational design, directed evolution, and computational methods and how these methods can be applied to improving the characteristics of peptides. We also provide a discussion of engineering the thermodynamic stability, self‐assembly, reduced aggregation, proteolytic stability, and binding affinity and specificity of peptides, along with a perspective on future directions in engineering therapeutic peptides.

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Design of Stable α-Helical Peptides and Thermostable Proteins in Biotechnology and Biomedicine

Cited by 36 publications

References 113 publications

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

Increases in Hydrophilicity and Charge on the Polar Face of Alyteserin 1c Helix Change its Selectivity towards Gram-Positive Bacteria

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide

Beyond function: Engineering improved peptides for therapeutic applications

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