Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality
Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertio...
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Published in | Journal of molecular biology Vol. 404; no. 2; pp. 232 - 246 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
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Elsevier Ltd
26.11.2010
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Abstract | Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. This newly discovered evolutionary origin explains both why π-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why they tend to be associated with function. An analysis of π-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative π-helix-containing primordial precursor, a “missing link” intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices that we term a “peristaltic-like shift.” This new understanding of π-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid in tracing the evolution of many protein families, guide investigations of protein and π-helix functionality, and contribute additional tools to the protein engineering toolkit.
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► Most π-helices are evolutionarily derived from α-helices via a one-residue insertion. ► Because they occur in the midst of α-helices, over 95% of π-helices are not annotated. ► π-Helices are useful for guiding insight into a protein's origin and functionality. ► A precursor with a novel diiron center is proposed for the ferritin-like superfamily. |
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AbstractList | Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. This newly discovered evolutionary origin explains both why π-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why they tend to be associated with function. An analysis of π-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative π-helix-containing primordial precursor, a "missing link" intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices that we term a "peristaltic-like shift." This new understanding of π-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid in tracing the evolution of many protein families, guide investigations of protein and π-helix functionality, and contribute additional tools to the protein engineering toolkit. Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. This newly discovered evolutionary origin explains both why π-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why they tend to be associated with function. An analysis of π-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative π-helix-containing primordial precursor, a “missing link” intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices that we term a “peristaltic-like shift.” This new understanding of π-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid in tracing the evolution of many protein families, guide investigations of protein and π-helix functionality, and contribute additional tools to the protein engineering toolkit. [Display omitted] ► Most π-helices are evolutionarily derived from α-helices via a one-residue insertion. ► Because they occur in the midst of α-helices, over 95% of π-helices are not annotated. ► π-Helices are useful for guiding insight into a protein's origin and functionality. ► A precursor with a novel diiron center is proposed for the ferritin-like superfamily. |
Author | Karplus, P. Andrew Arp, Daniel J. Cooley, Richard B. |
Author_xml | – sequence: 1 givenname: Richard B. surname: Cooley fullname: Cooley, Richard B. organization: Department of Biochemistry and Biophysics, 2011 Ag and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA – sequence: 2 givenname: Daniel J. surname: Arp fullname: Arp, Daniel J. organization: Department of Botany and Plant Pathology, 2082 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA – sequence: 3 givenname: P. Andrew surname: Karplus fullname: Karplus, P. Andrew email: karplusp@science.oregonstate.edu organization: Department of Biochemistry and Biophysics, 2011 Ag and Life Sciences Building, Oregon State University, Corvallis, OR 97331, USA |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20888342$$D View this record in MEDLINE/PubMed |
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Keywords | π-helix secondary structure BMM protein evolution ferritin-like superfamily RNR PH ToMO α-aneurism H-bond MMOH PDB |
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Snippet | Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that... |
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SubjectTerms | Amino Acid Sequence Evolution, Molecular ferritin-like superfamily Ferritins - chemistry Ferritins - genetics Hydrogen Bonding Models, Molecular Molecular Sequence Data Mutagenesis, Insertional Phylogeny protein evolution Protein Structure, Secondary - genetics Proteins - chemistry Proteins - genetics secondary structure Sequence Homology, Amino Acid Thermodynamics α-aneurism π-helix |
Title | Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality |
URI | https://dx.doi.org/10.1016/j.jmb.2010.09.034 https://www.ncbi.nlm.nih.gov/pubmed/20888342 |
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