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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
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Profile comparison revealed deviation from structural constraint at the positively selected sites.
Hiroyuki Oda1, Motonori Ota2, Hiroyuki Toh3
1Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.
Bio Systems
|July 23, 2016
Summary
Amino acid substitutions are influenced by various constraints, especially at sites under positive selection. This study reveals that positive selection often leads to deviations from structural constraints in proteins.
Area of Science:
- Computational biology
- Molecular evolution
- Protein structure and function
Background:
- Amino acid substitutions are shaped by a mix of constraints.
- Sites under positive selection exhibit accelerated amino acid substitutions.
- The interplay between positive selection and these constraints remains underexplored.
Purpose of the Study:
- To investigate the relationship between positive selection and constraints at amino acid sites.
- To differentiate between structural constraints and other constraints affecting amino acid substitutions.
- To analyze how positive selection impacts these constraint types.
Main Methods:
- Utilized computational biology approaches to analyze amino acid sequences and tertiary protein structures.
- Developed a method to separate mixture constraints into structural constraints and remaining constraints.
- Compared two profile matrices (20 x site length): one for mixed constraints (from sequence alignment) and one for structural constraints.
Main Results:
- Proteins under positive selection were analyzed using the profile comparison method.
- Results indicate that constraints at positively selected sites tend to deviate from structural constraints.
- This deviation suggests a distinct evolutionary pressure at these sites.
Conclusions:
- Positive selection influences amino acid site constraints, leading to a departure from purely structural limitations.
- The findings provide insights into the evolutionary dynamics of proteins under positive selection.
- This research enhances our understanding of how protein evolution is modulated by selection and structural factors.
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