Solution of Levinthal's Paradox and a Physical Theory of Protein Folding Times

被引:26
作者
Ivankov, Dmitry N. [1 ]
Finkelstein, Alexei V. [2 ,3 ,4 ]
机构
[1] Skolkovo Inst Sci & Technol, Ctr Life Sci, Moscow 121205, Russia
[2] Russian Acad Sci, Inst Prot Res, Pushchino 142290, Moscow Region, Russia
[3] Lomonosov Moscow State Univ, Biol Dept, Moscow 119192, Russia
[4] Lomonosov Moscow State Univ, Biotechnol Dept, Pushchino 142290, Moscow Region, Russia
基金
俄罗斯科学基金会;
关键词
protein folding; Levinthal's paradox; all-or-none" transition; free energy barrier; folding funnel; detailed balance principle; AMINO-ACID-SEQUENCE; SECONDARY STRUCTURE-CONTENT; TOPOMER SEARCH MODEL; AGAIN; VIEWS; TRANSITION-STATE; CONTACT ORDER; FIREFLY LUCIFERASE; NEURAL-NETWORKS; RATES; PREDICTION;
D O I
10.3390/biom10020250
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
"How do proteins fold?" Researchers have been studying different aspects of this question for more than 50 years. The most conceptual aspect of the problem is how protein can find the global free energy minimum in a biologically reasonable time, without exhaustive enumeration of all possible conformations, the so-called "Levinthal's paradox." Less conceptual but still critical are aspects about factors defining folding times of particular proteins and about perspectives of machine learning for their prediction. We will discuss in this review the key ideas and discoveries leading to the current understanding of folding kinetics, including the solution of Levinthal's paradox, as well as the current state of the art in the prediction of protein folding times.
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页数:19
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共 101 条
  • [41] GROUND-STATE OF RANDOM COPOLYMERS AND THE DISCRETE RANDOM ENERGY-MODEL
    GUTIN, AM
    SHAKHNOVICH, EI
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (10) : 8174 - 8177
  • [42] GUTTE B, 1971, J BIOL CHEM, V246, P1922
  • [43] A CORRELATION OF REACTION RATES
    HAMMOND, GS
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1955, 77 (02) : 334 - 338
  • [44] Monitoring cotranslational protein folding in mammalian cells at codon resolution
    Han, Yan
    David, Alexandre
    Liu, Botao
    Magadan, Javier G.
    Bennink, Jack R.
    Yewdell, Jonathan W.
    Qian, Shu-Bing
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (31) : 12467 - 12472
  • [45] Cotranslational protein folding on the ribosome monitored in real time
    Holtkamp, Wolf
    Kokic, Goran
    Jaeger, Marcus
    Mittelstaet, Joerg
    Komar, Anton A.
    Rodnina, Marina V.
    [J]. SCIENCE, 2015, 350 (6264) : 1104 - 1107
  • [46] NEURAL NETWORKS AND PHYSICAL SYSTEMS WITH EMERGENT COLLECTIVE COMPUTATIONAL ABILITIES
    HOPFIELD, JJ
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES, 1982, 79 (08): : 2554 - 2558
  • [47] Prediction of protein folding rates from simplified secondary structure alphabet
    Huang, Jitao T.
    Wang, Titi
    Huang, Shanran R.
    Li, Xin
    [J]. JOURNAL OF THEORETICAL BIOLOGY, 2015, 383 : 1 - 6
  • [48] Amino acid sequence predicts folding rate for middle-size two-state proteins
    Huang, JT
    Tian, J
    [J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006, 63 (03) : 551 - 554
  • [49] Analysis and prediction of protein folding rates using quadratic response surface models
    Huang, Liang-Tsung
    Gromiha, M. Michael
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2008, 29 (10) : 1675 - 1683
  • [50] Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
    Ingolia, Nicholas T.
    Lareau, Liana F.
    Weissman, Jonathan S.
    [J]. CELL, 2011, 147 (04) : 789 - 802