title: Frozen in Time: The History of Proteins.
abstract: The ribosome is imprinted with a detailed molecular chronology of the origins and early evolution of proteins. Here we show that when arranged by evolutionary phase of ribosomal evolution, ribosomal protein (rProtein) segments reveal an atomic level history of protein folding. The data support a model in which aboriginal oligomers evolved into globular proteins in a hierarchical step-wise process. Complexity of assembly and folding of polypeptide increased incrementally in concert with expansion of rRNA. (i) Short random coil proto-peptides bound to rRNA, and (ii) lengthened over time and coalesced into β-β secondary elements. These secondary elements (iii) accreted and collapsed, primarily into β-domains. Domains (iv) accumulated and gained complex super-secondary structures composed of mixtures of α-helices and β-strands. Early protein evolution was guided and accelerated by interactions with rRNA. rRNA and proto-peptide provided mutual protection from chemical degradation and disassembly. rRNA stabilized polypeptide assemblies, which evolved in a stepwise process into globular domains, bypassing the immense space of random unproductive sequences. Coded proteins originated as oligomers and polymers created by the ribosome, on the ribosome and for the ribosome. Synthesis of increasingly longer products was iteratively coupled with lengthening and maturation of the ribosomal exit tunnel. Protein catalysis appears to be a late byproduct of selection for sophisticated and finely controlled assembly.
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Kovacs
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA.
authors.forename: Anton S
authors.initials: AS
authors.lastname: Petrov
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA.
authors.forename: Kathryn A
authors.initials: KA
authors.lastname: Lanier
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA.
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
mesh_terms: D001665:Binding Sites / Q000235:genetics; D019143:Evolution, Molecular; D008958:Models, Molecular; D000069497:Origin of Life; D017510:Protein Folding; D017433:Protein Structure, Secondary / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism; D013329:Structure-Activity Relationship
chemical_list: D012335:RNA, Ribosomal; D012269:Ribosomal Proteins
keywords: origin of life; origins of protein folding; protein evolution; ribosomal origins and evolution; ribosomal protein; β-harpin