Fred E. Cohen

University of California, San Francisco

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Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Stanley B. Prusiner

University of California, San Francisco

Stanley B. Prusiner

University of California, San Francisco

Michael A. Baldwin

University of California, San Francisco

Jack Nguyen

Cincinnati Children's Hospital Medical Center

Scott Presnell

University of Washington

Stephen J. DeArmond

University of California, San Francisco

Robert J. Fletterick

University of California, San Francisco

Valerie Daggett

University of Washington

Michael R. Scott

University of British Columbia

Olivier Lichtarge

Baylor College of Medicine

Cooperative Institutions

University of California, San Francisco

Institute for Neurodegenerative Disorders

German Center for Neurodegenerative Diseases

University of California, Berkeley

University of California System

University of California, San Diego

Los Alamos National Laboratory

Harvard University

Institute of Molecular Biology and Biophysics

Massachusetts Institute of Technology

Author Statistics

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Citation

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Research Field

Conformational Transformations in Peptides Containing Two Putative α-Helices of the Prion Protein

Journal of Molecular Biology (1995)

Hong Zhang Kiyotoshi Kaneko Jack Nguyen Tatiana L. Livshits Michael A. Baldwin

Beta sheet

Sodium dodecyl sulfate

10.1006/jmbi.1995.0395

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Citations (178)

Prions, peptides and protein misfolding

Molecular Medicine Today (2000)

Fred E. Cohen

10.1016/s1357-4310(00)01740-8

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Citations (13)

Topological distribution of four-alpha-helix bundles.

Proceedings of the National Academy of Sciences (1989)

Scott Presnell Fred E. Cohen

The four-alpha-helix bundle, a common structural motif in globular proteins, provides an excellent forum for the examination of predictive constraints for protein backbone topology. An exhaustive examination of the Brookhaven Crystallographic Protein Data Bank and other literature sources has lead to the discovery of 20 putative four-alpha-helix bundles. Application of an analytical method that examines the difference between solvent-accessible surface areas in packed and partially unpacked bundles reduced the number of structures to 16. Angular requirements further reduced the list of bundles to 13. In 12 of these bundles, all pairs of neighboring helices were oriented in an anti-parallel fashion. This distribution is in accordance with structure types expected if the helix macro dipole effect makes a substantial contribution to the stability of the native structure. The characterizations and classifications made in this study prompt a reevaluation of constraints used in structure prediction efforts.

Helix (gastropod)

Helix bundle

Alpha helix

Globular protein

Structural motif

10.1073/pnas.86.17.6592

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Citations (189)

Origins of structural diversity within sequentially identical hexapeptides

Protein Science (1993)

B. I. Cohen Scott Presnell Fred E. Cohen

Abstract Efforts to predict protein secondary structure have been hampered by the apparent structural plasticity of local amino acid sequences. Kabsch and Sander (1984, Proc. Natl. Acad. Sci. USA 81 , 1075–1078) articulated this problem by demonstrating that identical pentapeptide sequences can adopt distinct structures in different proteins. With the increased size of the protein structure database and the availability of new methods to characterize structural environments, we revisit this observation of structural plasticity. Within a set of proteins with less than 50% sequence identity, 59 pairs of identical hexapeptide sequences were identified. These local structures were compared and their surrounding structural environments examined. Within a protein structural class ( α/α, β/β, α/β, α + β ), the structural similarity of sequentially identical hexapeptides usually is preserved. This study finds eight pairs of identical hexapeptide sequences that adopt β ‐strand structure in one protein and α ‐helical structure in the other. In none of the eight cases do the members of these sequence pairs come from proteins within the same folding class. These results have implications for class dependent secondary structure prediction algorithms.

Pentapeptide repeat

Structural bioinformatics

Structural plasticity

Sequence (biology)

Folding (DSP implementation)

Structural alignment

Loop modeling

Protein primary structure

10.1002/pro.5560021213

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Citations (97)

Strain‐specified relative conformational stability of the scrapie prion protein

Protein Science (2001)

David Peretz Michael R. Scott Darlene Groth R. Anthony Williamson Dennis R. Burton

Abstract Studies of prion biology and diseases have elucidated several new concepts, but none was more heretical than the proposal that the biological properties that distinguish different prion strains are enciphered in the disease‐causing prion protein (PrP Sc ). To explore this postulate, we examined the properties of PrP Sc from eight prion isolates that propagate in Syrian hamster (SHa). Using resistance to protease digestion as a marker for the undenatured protein, we examined the conformational stabilities of these PrP Sc molecules. All eight isolates showed sigmoidal patterns of transition from native to denatured PrP Sc as a function of increasing guanidine hydrochloride (GdnHCl) concentration. Half‐maximal denaturation occurred at a mean value of 1.48 M GdnHCl for the Sc237, HY, SHa(Me7), and MT‐C5 isolates, all of which have ∼75‐d incubation periods; a concentration of 1.08 M was found for the DY strain with a ∼170‐d incubation period and ∼1.25 M for the SHa(RML) and 139H isolates with ∼180‐d incubation periods. A mean value of 1.39 M GdnHCl for the Me7‐H strain with a ∼320‐d incubation period was found. Based on these results, the eight prion strains segregated into four distinct groups. Our results support the unorthodox proposal that distinct PrP Sc conformers encipher the biological properties of prion strains.

Incubation period

Strain (injury)

Guanidine

Proteinase K

Denaturation (fissile materials)

Conformational isomerism

10.1110/ps.39201

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Citations (245)

Prion Protein Peptides Induce .alpha.-Helix to .beta.-Sheet Conformational Transitions

Biochemistry (1995)

Jack Nguyen Michael A. Baldwin Fred E. Cohen Stanley B. Prusiner

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrion Protein Peptides Induce .alpha.-Helix to .beta.-Sheet Conformational TransitionsJack Nguyen, Michael A. Baldwin, Fred E. Cohen, and Stanley B. PrusinerCite this: Biochemistry 1995, 34, 13, 4186–4192Publication Date (Print):April 4, 1995Publication History Published online1 May 2002Published inissue 4 April 1995https://pubs.acs.org/doi/10.1021/bi00013a006https://doi.org/10.1021/bi00013a006research-articleACS PublicationsRequest reuse permissionsArticle Views1180Altmetric-Citations165LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts

Beta sheet

BETA (programming language)

Alpha (finance)

Alpha helix

Helix (gastropod)

10.1021/bi00013a006

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Citations (194)

Scrapie prions: a three-dimensional model of an infectious fragment

Folding and Design (1996)

Ziwei Huang Stanley B. Prusiner Fred E. Cohen

Folding (DSP implementation)

10.1016/s1359-0278(96)00007-7

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Citations (193)

X-ray Diffraction of Scrapie Prion Rods and PrP Peptides

Journal of Molecular Biology (1995)

Jack Nguyen Hideyo Inouye Michael A. Baldwin Robert J. Fletterick Fred E. Cohen

Residue (chemistry)

Proteinase K

Histone octamer

10.1006/jmbi.1995.0507

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Citations (166)

Conformational switching in designed peptides: the helix/sheet transition

Folding and Design (1996)

Robert Cerpa Fred E. Cohen Irwin D. Kuntz

Antiparallel (mathematics)

Beta sheet

Helix (gastropod)

Conformational change

Alpha helix

10.1016/s1359-0278(96)00018-1

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Citations (111)

Hydrogen bonds involving sulfur atoms in proteins

Proteins Structure Function and Bioinformatics (1991)

Lydia M. Gregoret Stephen D. Rader Robert J. Fletterick Fred E. Cohen

Abstract Intrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high‐resolution protein structures in order to evaluate the prevalence and geometry of sulfur‐containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians intersted in protein structure and protein engineering.

Globular protein

Low-barrier hydrogen bond

10.1002/prot.340090204

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Citations (241)