Principles of protein folding--a perspective from simple exact models

Protein Science : a Publication of the Protein Society
K A DillHue Sun Chan

Abstract

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which ...Continue Reading

References

Jan 1, 1979·Advances in Protein Chemistry·P L Privalov
Feb 1, 1978·Proceedings of the National Academy of Sciences of the United States of America·N Go, H Taketomi
Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jun 17, 1976·Nature·Michael Levitt, C Chothia
Apr 1, 1976·Nature·M Karplus, D L Weaver
Dec 11, 1992·Biochimica Et Biophysica Acta·J A Killian
Feb 1, 1992·Protein Science : a Publication of the Protein Society·D ShortleK A Dill
Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·M S Briggs, H Roder
Oct 1, 1992·Current Opinion in Biotechnology·K Kuwajima
Apr 3, 1992·Science·T E Creighton
Oct 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·J S Weissman, P S Kim
Oct 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R A GoldsteinP G Wolynes
Oct 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·R J SimonC K Marlowe
Aug 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·J VilaH A Scheraga
Jan 1, 1992·Annual Review of Biophysics and Biomolecular Structure·S W Englander, L Mayne
Jan 1, 1992·Annual Review of Biophysics and Biomolecular Structure·J M Scholtz, R L Baldwin
Sep 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·P E LeopoldJ N Onuchic
Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·Q X HuaM A Weiss
Apr 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·D A Hinds, Michael Levitt
May 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·D W HeinzB W Matthews
May 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·K Yue, K A Dill
May 25, 1992·Proceedings of the National Academy of Sciences of the United States of America·L Zhong, W C Johnson
Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R A GoldsteinP G Wolynes
May 11, 1992·Biophysical Journal·S Chacko, G N Phillips
Jul 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·T P Creamer, G D Rose
Jul 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·M H HaoH A Scheraga
Jun 1, 1992·Biopolymers·J D Honeycutt, D Thirumalai
Oct 5, 1991·Journal of Molecular Biology·M F Jeng, S W Englander
Dec 5, 1991·Journal of Molecular Biology·Y Goto, S Nishikiori
Jul 22, 1991·Proceedings. Biological Sciences·D J Lipman, W J Wilbur
Jan 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R ZwanzigB Bagchi
Jan 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·J M FlanaganD M Engelman
Dec 13, 1991·Science·H FrauenfelderP G Wolynes
Jan 1, 1991·Methods in Enzymology·J F Reidhaar-OlsonR T Sauer

Citations

Sep 1, 1995·Protein Science : a Publication of the Protein Society·D W Miller, K A Dill
Jan 1, 1996·Protein Science : a Publication of the Protein Society·L Toma, S Toma
Feb 1, 1996·Protein Science : a Publication of the Protein Society·K Yue, K A Dill
Jun 1, 1996·Protein Science : a Publication of the Protein Society·K K KoretkeP G Wolynes
Aug 1, 1996·Protein Science : a Publication of the Protein Society·M MunsonL Regan
Sep 1, 1996·Protein Science : a Publication of the Protein Society·C J Camacho, D Thirumalai
Oct 1, 1996·Protein Science : a Publication of the Protein Society·T C Beutler, K A Dill
Nov 1, 1996·Protein Science : a Publication of the Protein Society·J O Wrabl, D Shortle
Feb 1, 1997·Protein Science : a Publication of the Protein Society·N HirotaY Goto
Apr 1, 1997·Protein Science : a Publication of the Protein Society·K J Frye, C A Royer
Jul 1, 1997·Protein Science : a Publication of the Protein Society·M HoshinoY Goto
Jul 1, 1997·Protein Science : a Publication of the Protein Society·F TaniE Doi
Jul 1, 1997·Protein Science : a Publication of the Protein Society·J X Zhang, D P Goldenberg
Aug 1, 1997·Protein Science : a Publication of the Protein Society·R L Dunbrack, F E Cohen
Sep 23, 1997·Protein Science : a Publication of the Protein Society·Y FezouiJ J Osterhout
Oct 23, 1997·Protein Science : a Publication of the Protein Society·D W Miller, K A Dill
May 6, 1998·Protein Science : a Publication of the Protein Society·D O Alonso, V Daggett
May 6, 1998·Protein Science : a Publication of the Protein Society·T Konno
Oct 7, 1998·Protein Science : a Publication of the Protein Society·C V SindelarB Tidor
Dec 29, 1998·Protein Science : a Publication of the Protein Society·M C DemirelI Bahar
Dec 29, 1998·Protein Science : a Publication of the Protein Society·O KeskinR L Jernigan
Dec 29, 1998·Protein Science : a Publication of the Protein Society·Y X FanC L Tsou
Dec 29, 1998·Protein Science : a Publication of the Protein Society·P GuptaA C Voegler
Apr 10, 2012·European Biophysics Journal : EBJ·Agata WawrzkiewiczZbigniew J Grzywna
Aug 12, 2009·Journal of Biological Physics·Jingfa LiuZhaoxia Liu
Mar 16, 2013·Cell Biochemistry and Biophysics·Chiranjib Chakraborty, Alok Agrawal
Apr 3, 2004·Biophysical Chemistry·S O Yesylevskyy, A P Demchenko
Oct 23, 2012·Cell Reports·Bin Zhang, Thomas F Miller
Feb 12, 2004·Computational Biology and Chemistry·M Llabrés, F Rosselló
Oct 1, 2003·Journal of Molecular Biology·Rahul BanerjeePartha Saha
Apr 20, 2004·Current Opinion in Structural Biology·Yu Xia, Michael Levitt
Oct 29, 2000·Biophysical Journal·A Irbäck, E Sandelin
Jun 11, 2002·Journal of Molecular Biology·Jie LiuMin Lu
Sep 7, 2002·Journal of Molecular Biology·Karin A CrowhurstJulie D Forman-Kay
May 6, 2003·Journal of Molecular Biology·Ke Fan, Wei Wang
Aug 23, 2003·Biophysical Chemistry·Jin ChenDelu Zhao
Mar 21, 2000·Biophysical Chemistry·S M Patra, S Vishveshwara
Aug 1, 1996·Current Opinion in Biotechnology·C A Schiffer, V Dötsch
Apr 1, 1996·Current Opinion in Structural Biology·R L Jernigan, I Bahar
Apr 1, 1996·Current Opinion in Structural Biology·P Koehl, M Delarue
Feb 1, 1997·Current Opinion in Structural Biology·H Roder, W Colón
Apr 1, 1997·Current Opinion in Structural Biology·S VajdaJ Novotny

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Nodding Syndrome

Nodding Syndrome is a neurological and epileptiform disorder characterized by psychomotor, mental, and growth retardation. Discover the latest research on Nodding Syndrome here.

LRRK2 & Microtubules

Mutations in the LRRK2 gene are risk-factors for developing Parkinson’s disease (PD). LRRK2 mutations in PD have been shown to enhance its association with microtubules. Here is the latest research.

Related Papers

Current Opinion in Structural Biology
M Karplus, A Sali
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
B Berger, T Leighton
Proceedings of the National Academy of Sciences of the United States of America
K YueK A Dill
© 2021 Meta ULC. All rights reserved