title: Compact Structure Patterns in Proteins.
abstract: Globular proteins typically fold into tightly packed arrays of regular secondary structures. We developed a model to approximate the compact parallel and antiparallel arrangement of α-helices and β-strands, enumerated all possible topologies formed by up to five secondary structural elements (SSEs), searched for their occurrence in spatial structures of proteins, and documented their frequencies of occurrence in the PDB. The enumeration model grows larger super-secondary structure patterns (SSPs) by combining pairs of smaller patterns, a process that approximates a potential path of protein fold evolution. The most prevalent SSPs are typically present in superfolds such as the Rossmann-like fold, the ferredoxin-like fold, and the Greek key motif, whereas the less frequent SSPs often possess uncommon structure features such as split β-sheets, left-handed connections, and crossing loops. This complete SSP enumeration model, for the first time, allows us to investigate which theoretically possible SSPs are not observed in available protein structures. All SSPs with up to four SSEs occurred in proteins. However, among the SSPs with five SSEs, approximately 20% (218) are absent from existing folds. Of these unobserved SSPs, 80% contain two or more uncommon structure features. To facilitate future efforts in protein structure classification, engineering, and design, we provide the resulting patterns and their frequency of occurrence in proteins at: http://prodata.swmed.edu/ssps/.
authors: Department 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.
authors: Bhadrachalam
authors: B
authors: Chitturi
authors: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA.
authors: Shuoyong
authors: S
authors: Shi
authors: Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA.
authors: Lisa N
authors: LN
authors: Kinch
authors: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA. Electronic address: grishin@chop.swmed.edu.
authors: Nick V
authors: NV
authors: Grishin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: fold; helix; secondary structure elements; strand; super-secondary structure pattern