Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins

被引:47
作者
Andrews, Benjamin T. [1 ]
Capraro, Dominique T. [3 ]
Sukowska, Joanna I. [4 ]
Onuchic, Jose N. [2 ]
Jennings, Patricia A. [3 ]
机构
[1] Univ Washington, Dept Med Chem, Seattle, WA 98195 USA
[2] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 USA
[3] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA
[4] Univ Warsaw, Fac Chem, PL-02093 Warsaw, Poland
基金
美国国家科学基金会;
关键词
GREEN-FLUORESCENT PROTEIN; ENERGY LANDSCAPE; KNOTTED PROTEIN; CIRCULAR PERMUTATION; FOLDING MECHANISMS; GFP; CHROMOPHORE; PATHWAYS; MOLECULE; AEQUOREA;
D O I
10.1021/jz301893w
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of the proteins. Oftentimes, these regions are introduced into the protein scaffold for function and increase frustration in the otherwise smooth-funneled landscape. Interestingly, while functional regions add complexity to folding landscapes, they may also contribute to a unique behavior referred to as hysteresis. 'While hysteresis is predicted to be rare, it is observed in various proteins, including proteins containing a unique peptide cyclization to form a fluorescent chromophore as well as proteins containing a knotted topology in their native fold. Here, hysteresis is demonstrated to be a consequence of the decoupling of unfolding events from the isomerization or hula-twist of a chromophore in one protein and the untying of the knot in a second protein system. The question now is can hysteresis be a marker for the interplay of landscapes where complex folding and functional regions overlap?
引用
收藏
页码:180 / 188
页数:9
相关论文
共 97 条
[1]   Non-random usage of 'degenerate' codons is related to protein three-dimensional structure [J].
Adzhubei, AA ;
Adzhubei, IA ;
Krasheninnikov, IA ;
Neidle, S .
FEBS LETTERS, 1996, 399 (1-2) :78-82
[2]   Structure and mechanism of the reversible photoswitch of a fluorescent protein [J].
Andresen, M ;
Wahl, MC ;
Stiel, AC ;
Gräter, F ;
Schäfer, LV ;
Trowitzsch, S ;
Weber, G ;
Eggeling, C ;
Grubmüller, H ;
Hell, SW ;
Jakobs, S .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (37) :13070-13074
[3]   The dual-basin landscape in GFP folding [J].
Andrews, Benjamin T. ;
Gosavi, Shachi ;
Finke, John M. ;
Onuchic, Jose N. ;
Jennings, Patricia A. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (34) :12283-12288
[4]   The rough energy landscape of superfolder GFP is linked to the chromophore [J].
Andrews, Benjamin T. ;
Schoenfish, Andrea R. ;
Roy, Melinda ;
Waldo, Geoffrey ;
Jennings, Patricia A. .
JOURNAL OF MOLECULAR BIOLOGY, 2007, 373 (02) :476-490
[5]   Chromophore Packing Leads to Hysteresis in GFP [J].
Andrews, Benjamin T. ;
Roy, Melinda ;
Jennings, Patricia A. .
JOURNAL OF MOLECULAR BIOLOGY, 2009, 392 (01) :218-227
[6]   Circular permutation and receptor insertion within green fluorescent proteins [J].
Baird, GS ;
Zacharias, DA ;
Tsien, RY .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (20) :11241-11246
[7]   Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures [J].
Barondeau, DP ;
Putnam, CD ;
Kassmann, CJ ;
Tainer, JA ;
Getzoff, ED .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (21) :12111-12116
[8]   Temperature-induced denaturation and renaturation of triosephosphate isomerase from Saccharomyces cerevisiae:: Evidence of dimerization coupled to refolding of the thermally unfolded protein [J].
Benítez-Cardoza, CG ;
Rojo-Domínguez, A ;
Hernández-Arana, A .
BIOCHEMISTRY, 2001, 40 (30) :9049-9058
[9]   Navigating the Folding Energy Landscape of Green Fluorescent Protein [J].
Bertz, Morten ;
Kunfermann, Andrea ;
Rief, Matthias .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2008, 47 (43) :8192-8195
[10]   A Stevedore's Protein Knot [J].
Boelinger, Daniel ;
Sulkowska, Joanna I. ;
Hsu, Hsiao-Ping ;
Mirny, Leonid A. ;
Kardar, Mehran ;
Onuchic, Jose N. ;
Virnau, Peter .
PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (04)