Folding by numbers: primary sequence statistics and their use in studying protein folding

Abstract

The exponential growth over the past several decades in the quantity of both primary sequence data available and the number of protein structures determined has provided a wealth of information describing the relationship between protein primary sequence and tertiary structure. This growing repository of data has served as a prime source for statistical analysis, where underlying relationships between patterns of amino acids and protein structure can be uncovered. Here, we survey the main statistical approaches that have been used for identifying patterns within protein sequences, and discuss sequence pattern research as it relates to both secondary and tertiary protein structure. Limitations to statistical analyses are discussed, and a context for their role within the field of protein folding is given. We conclude by describing a novel statistical study of residue patterning in beta-strands, which finds that hydrophobic (i,i+2) pairing in beta-strands occurs more often than expected at locations near strand termini. Interpretations involving beta-sheet nucleation and growth are discussed.

Keywords: Primary Sequence; Protein Folding; Sequence-Structure Relationship.

Figure 1.

Hydrophobic and hydrophilic coupling within β-strands.

Figure 2.

Position-specific hydrophobic coupling within β-strands.