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Compact Structure Patterns in Proteins.

Bhadrachalam Chitturi1, Shuoyong Shi2, Lisa N Kinch3

  • 1Department of Computer Science and Engineering, Amrita School of Engineering, Amritapuri, Amrita Vishwa Vidyapeetham, Amrita University, India; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA; Departments of Computer Science, University of Texas at Dallas, Richardson, TX 75083, USA.

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|August 8, 2016
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Summary
This summary is machine-generated.

Researchers modeled protein folding by enumerating possible arrangements of secondary structural elements (SSEs). They found that while all combinations with up to four SSEs exist in proteins, 20% of five-SSE combinations are notably absent, often due to complex structural features.

Keywords:
foldhelixsecondary structure elementsstrandsuper-secondary structure pattern

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Globular proteins fold into compact structures of alpha-helices and beta-strands.
  • Understanding the complete set of possible protein folds is crucial for predicting and designing protein structures.

Purpose of the Study:

  • To develop a model for enumerating all possible super-secondary structure patterns (SSPs) formed by up to five secondary structural elements (SSEs).
  • To investigate the occurrence and frequency of these theoretical SSPs in known protein structures within the Protein Data Bank (PDB).
  • To identify which theoretically possible SSPs are absent in existing protein folds and analyze their structural characteristics.

Main Methods:

  • Developed a computational model to systematically enumerate all possible parallel and antiparallel arrangements of alpha-helices and beta-strands.
  • Grew larger SSPs by combining smaller patterns, simulating a potential evolutionary path of protein folds.
  • Searched the PDB for occurrences of enumerated SSPs and documented their frequencies.

Main Results:

  • All theoretical SSPs comprising up to four SSEs were found to occur in known protein structures.
  • Approximately 20% (218) of SSPs with five SSEs are absent from the PDB.
  • The majority (80%) of these unobserved five-SSE SSPs contain uncommon structural features, such as split beta-sheets or crossing loops.

Conclusions:

  • The study provides a comprehensive catalog of theoretical SSPs and their prevalence in proteins.
  • The findings reveal that complex structural features are associated with unobserved protein folds.
  • This enumeration model serves as a valuable resource for protein structure classification, engineering, and design.