Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role

Sælensminde, Gisle; Halskau, Øyvind; Jonassen, Inge

doi:10.1007/s00792-008-0192-4

Cited by 56 publications

(49 citation statements)

References 43 publications

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“…Another study that analyzed the sequence of nearly 400 cold-adapted proteins, also reported similar differences at the protein surface, consistent with alterations in amino acid contacts with the solvent [31]. Changes at the surface resulted in greater entropic effects rather than specific effects like diminished numbers of salt bridges.…”

Section: Discussionmentioning

confidence: 64%

Amino Acid Substitutions in Cold-Adapted Proteins from Halorubrum lacusprofundi, an Extremely Halophilic Microbe from Antarctica

et al. 2013

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The halophilic Archaeon Halorubrum lacusprofundi, isolated from the perennially cold and hypersaline Deep Lake in Antarctica, was recently sequenced and compared to 12 Haloarchaea from temperate climates by comparative genomics. Amino acid substitutions for 604 H. lacusprofundi proteins belonging to conserved haloarchaeal orthologous groups (cHOGs) were determined and found to occur at 7.85% of positions invariant in proteins from mesophilic Haloarchaea. The following substitutions were observed most frequently: (a) glutamic acid with aspartic acid or alanine; (b) small polar residues with other small polar or non-polar amino acids; (c) small non-polar residues with other small non-polar residues; (d) aromatic residues, especially tryptophan, with other aromatic residues; and (e) some larger polar residues with other similar residues. Amino acid substitutions for a cold-active H. lacusprofundi β-galactosidase were then examined in the context of a homology modeled structure at residues invariant in homologous enzymes from mesophilic Haloarchaea. Similar substitutions were observed as in the genome-wide approach, with the surface accessible regions of β-galactosidase displaying reduced acidity and increased hydrophobicity, and internal regions displaying mainly subtle changes among smaller non-polar and polar residues. These findings are consistent with H. lacusprofundi proteins displaying amino acid substitutions that increase structural flexibility and protein function at low temperature. We discuss the likely mechanisms of protein adaptation to a cold, hypersaline environment on Earth, with possible relevance to life elsewhere.

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Section: Discussionmentioning

confidence: 64%

Amino Acid Substitutions in Cold-Adapted Proteins from Halorubrum lacusprofundi, an Extremely Halophilic Microbe from Antarctica

et al. 2013

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“…Higher proline percentage for thermostable protein shows its pronounced role in enhancing thermostability as it is more rigid than other amino acids and reduces the entropy of the main chain polypeptide decreasing the chance of unfolding at elevated temperatures [46]. The results in the present study have clearly showed that proline is higher in both ends of temperature when compared to moderate inhabitant.…”

Section: Discussionsupporting

confidence: 51%

In Silico Analysis of β-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation

Kumar

Sharma

Bhalla

2014

Journal of Amino Acids

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β-D-Galactosidases (EC 3.2.1.23) hydrolyze the terminal nonreducing β-D-galactose residues in β-D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial β-galactosidase protein sequences, six each from psychrophilic, mesophilic, and thermophilic microbes, were analyzed. Primary structure reveals alanine, glycine, serine, and arginine to be higher in psychrophilic β-galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic β-galactosidases. Cold active β-galactosidase has a strong preference towards tiny and small amino acids, whereas high temperature inhabitants had higher content of basic and aromatic amino acids. Thermophilic β-galactosidases have higher percentage of α-helix region responsible for temperature tolerance while cold loving β-galactosidases had higher percentage of sheet and coil region. Secondary structure analysis revealed that charged and aromatic amino acids were significant for sheet region of thermophiles. Alanine was found to be significant and high in the helix region of psychrophiles and valine counters in thermophilic β-galactosidase. Coil region of cold active β-galactosidase has higher content of tiny amino acids which explains their high catalytic efficiency over their counterparts from thermal habitat. The present study has revealed the preference or prevalence of certain amino acids in primary and secondary structure of psychrophilic, mesophilic, and thermophilic β-galactosidase.

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“…However, a very high abundance of a single species or members of the phylum will influence clustering of samples based on phylum level abundances. Previous studies identified differences in the amino acid composition between mesophiles and thermophiles [35], [36], which originated at differences in genomic GC content as well as changes of relative frequencies of certain amino acids that affected the thermal stability of the protein [37], [38]. The most variability of the amino acid profiles of the thermophiles was well justified by the genomic GC content, temperature having only little significant effect [39].…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India

2017

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Various aspects of hot springs at Bakreshwar (Lat. 23°52′48″N; Long. 87°22′40″E) in West Bengal, India have been investigated since the middle of 20th century, but comprehending the complete diversity and the complexity of the microbial population therein has been in the continuing process. Some of these microorganisms are found to have immense industrial importance. Microbes generally exist in milieus of varying complexities and diversities. Attempting the usually employed cultivation-based techniques in experimentation with those microbes had confronted various limitations. To overcome these limitations a strategy based on high-throughput sequencing of 16S rRNA gene amplicon analysis was employed for studying the differential diversity and the detailed nature of microbial population of the two hot springs of Bakreshwar (54 °C & 65 °C). Paired-end libraries of amplified V-3 hyper-variable 16S rDNA fragments from sets of samples that varied in their contents, ranging from a single bacterium to highly complex communities were sequenced. The comparison revealed the differential aspects in the two hot spring waters; the samples at 54 °C showed the bacterial phylum Firmicutes (65.85%) and Synergistetes (27.24%) predominating and those from hot spring water at 65 °C showed the abundance of the phyla Firmicutes (96.10%) and Proteobacteria (3.36%). The presence of Archaea in the hot springs could not be ascertained.

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Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role

Cited by 56 publications

References 43 publications

Amino Acid Substitutions in Cold-Adapted Proteins from Halorubrum lacusprofundi, an Extremely Halophilic Microbe from Antarctica

Amino Acid Substitutions in Cold-Adapted Proteins from Halorubrum lacusprofundi, an Extremely Halophilic Microbe from Antarctica

In Silico Analysis of β-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India

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