Representation of amino acid sequences in terms of interaction energy in protein globules

Berezovsky, Igor N.; Tumanyan, V. G.; Ng, Esipova

doi:10.1016/s0014-5793(97)01346-x

Cited by 30 publications

(19 citation statements)

References 24 publications

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“…Specifically, prevalence of the nucleotide thymine in the second codon position and its strong correlation with OGT in Archaea is apparently a result of the demand on enrichement of Archaeal proteins with hydrophobic residues (Table 7). Noteworthy, a massive increase of van der Waals interactions (24,64) was found to be the cornerstone of the structure-based evolutionary strategy of protein thermostability in ancient species (29). In Bacterial proteins, however, there is an increase of the fractions of charged residues with OGT (Table 7).…”

Section: Discussionmentioning

confidence: 99%

“…Specifically, it has been claimed that it is essentially governed by the genome replication and DNA-repair mechanisms (19), is involved into lineage- and niche-specific molecular strategies of adaptation (17), drives a codon usage (20) and even amino acid composition (12–14,16). In the case of protein structure, distinct stabilizing interactions (24–28), their structural determinants (24,29–33) and contribution from different amino acid residues (22,24,25,29,34–36) have been studied extensively (37–40). However, until recently all the studies were focused around few proteins or small set of them, individual stabilizing interactions, or considered anecdotal cases of organisms thriving under normal or extreme temperatures.…”

Section: Introductionmentioning

confidence: 99%

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Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

Goncearenco

Berezovsky

2013

Nucleic Acids Research

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DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

Goncearenco

Berezovsky

2013

Nucleic Acids Research

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“…Two types of physical mechanisms that contribute to protein thermophily are distinguished as "structure-based" and "sequencebased" (19). The features associated with enhanced thermal stability include ionic interactions (20), increase in hydrophobicity and packing density (21,22), augmentation of hydrogen bonding and van der Waals interactions (23,24), and specific amino acid substitutions that stabilize protein structure at particularly critical locations (25).…”

mentioning

confidence: 99%

A Novel Mercuric Reductase from the Unique Deep Brine Environment of Atlantis II in the Red Sea

Sayed

Ghazy

Ferreira

et al. 2014

Journal of Biological Chemistry

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Background: Molecular features underlying enzyme function in extreme environments are poorly understood. Results: Identification of the basis for thermostability, halophilicity, and detoxification activity in a mercuric reductase from hot deep-sea brine. Conclusion: A small number of structural modifications accounts for the enzyme's robustness. Significance: This work defines novel adaptations that enable enzymes to cope with multiple abiotic stressors simultaneously.

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“…The energy of the pair-wise interactions is calculated for atoms belonging to residues separated by at least two amino acid residues. This is suf cient (Berezovskii et al, 1997a;Berezovsky et al, 1997b;Berezovskii and Tumanyan, 1995) for estimating the interactions between the adjacent regions of the globule. Only contacts between atoms were taken into consideration and appropriate energies were calculated if the distance lay in the range of values 2.5-5.0Å.…”

Section: Figmentioning

confidence: 99%

Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure

Berezovsky

Tumanyan

2000

Journal of Computational Biology

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The method of the representation of amino acid sequence by graph of the interactions energy between parts of spatial structure has been elaborated. Our method provides the possibility to establish the compatibility between each point of a polypeptide chain and the Van der Waals interactions energy of regions of a native globule adjacent to this amino acid residue. We have undertaken an exhaustive analysis of a set of proteins. Boundaries of domain and module structures have been found. Nonequivalence of different parts of sequences in respect to their contribution to stabilization of the spatial structure of the protein macromolecules has been revealed. On the basis of the number of energetic levels which are necessary to identify all independent parts of the globule, the contribution from each part of the sequence to stabilization of the spatial structure of the globule is defined. Thus, it has been found that the sequence of amino acid residues coincides with the sequence of the numerical values which can be used in turn in formal procedures, such as an alignment, a search of consensus, the recognition of composition peculiarities, etc. An example of the comparison of proteins with various sequence identities is considered to demonstrate the scheme of an alignment procedure.

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Representation of amino acid sequences in terms of interaction energy in protein globules

Cited by 30 publications

References 24 publications

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

A Novel Mercuric Reductase from the Unique Deep Brine Environment of Atlantis II in the Red Sea

Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure

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