Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

How the Protein Sequences Adapt to Function in Varied Temperatures? A Comparative Proteome Analyses of Microorganisms that Live in Varied Temperatures

In order to understand how protein sequences have adapted to optimal growth temperatures of their respective microorganisms, we have carried out a comparative sequence analysis of proteomes of four groups of microorganisms that live at a wide range of temperatures (sub-zero to higher than hundred °C) namely, psychrophilic (P), mesophilic (M), thermophilic (T), and hyperthermophilic (HT), organisms. We have used 24 bacterial proteomes, 6 each of P, M, T, and HT. Orthologous pairs of all available proteins were identified between proteomes using BLASTP search tool with < 10-5 expectation value > 40 bit scores. We have picked up alignments of all best possible single top hit for every protein sequence in a query proteome that has an ortholog in the subject proteome. The alignments were parsed to calculate amino acid substitution counts between the two orthologous proteins of respective proteomes. The substitution counts were normalized with respect to the composition of total amino acids in their respective proteomes.

For example, in the case of psychrophiles versus mesophiles, the frequency of substitutions was further used to calculate two types of likelihood log odd substitution scores (LOS):

The mutual substitution scores (LOS) of amino acids clearly show that the substitutions that lead to adaptation to cold temperatures are either overrepresented or avoided. In psychrophilic bacteria, serine, aspartic acid, threonine, and alanine are overrepresented in the coil regions of secondary structures, while glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic, and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. These findings would help future efforts in rationally designing and selecting mutations for psychrophilic properties in proteins of interest.

The observations from such analyses carried out for all pair-wise proteome comparisons such as Meso vs Thermo, Psychro vs Thermo, etc., will be discussed.

Boojala Vijay B. Reddy*
Raghu P. Metpally

The Laboratory of Bioinformatics and In Silico Drug Design
Queens College and Graduate Center of City University of New York
65-30 Kissena Blvd.
Flushing, NY 11367, USA

*Email: vijay@velgonda.cs.qc.cuny.edu