How to fold intricately: using theory and experiments to unravel the properties of knotted proteins

被引：77

作者：

Jackson, Sophie E. ^{[1
]}

Suma, Antonio ^{[2
]}

Micheletti, Cristian ^{[2
]}

机构：

[1] Univ Cambridge, Dept Chem, Cambridge CB2 1EW, England

[2] Scuola Int Super Studi Avanzati, SISSA, Via Bonomea 265, I-34136 Trieste, Italy

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2017年 / 42卷

关键词：

TOPOLOGICALLY COMPLEX PROTEINS; INFRARED FLUORESCENT PROTEIN; TRANSFER-RNA; ENERGY LANDSCAPE; TREFOIL KNOT; ACTIVE-SITE; MECHANISM; CONFORMATIONS; STATISTICS; ENZYME;

D O I：

10.1016/j.sbi.2016.10.002

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：

Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.

引用

页码：6 / 14

页数：9

共 68 条

[1] The Effect of Parkinson's-Disease-Associated Mutations on the Deubiquitinating Enzyme UCH-L1 [J].

Andersson, Fredrik I. ;

Werrell, Elizabeth F. ;

McMorran, Lindsay ;

Crone, William J. K. ;

Das, Chittarnajan ;

Hsu, Shang-Te Danny ;

Jackson, Sophie E. .

JOURNAL OF MOLECULAR BIOLOGY, 2011, 407 (02) :261-272

[2] Untangling the folding mechanism of the 52-knotted protein UCH-L3 [J].

Andersson, Fredrik I. ;

Pina, David G. ;

Mallam, Anna L. ;

Blaser, Georg ;

Jackson, Sophie E. .

FEBS JOURNAL, 2009, 276 (09) :2625-2635

[3] Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field [J].

Beccara, Silvio A. ;

Skrbic, Tatjana ;

Covino, Roberto ;

Micheletti, Cristian ;

Faccioli, Pietro .

PLOS COMPUTATIONAL BIOLOGY, 2013, 9 (03)

[4] The Protein Data Bank and the challenge of structural genomics [J].

Berman, HM ;

Bhat, TN ;

Bourne, PE ;

Feng, ZK ;

Gilliland, G ;

Weissig, H ;

Westbrook, J .

NATURE STRUCTURAL BIOLOGY, 2000, 7 (Suppl 11) :957-959

[5] 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)

[6] Tightening the Knot in Phytochrome by Single-Molecule Atomic Force Microscopy [J].

Bornschloegl, Thomas ;

Anstrom, David M. ;

Mey, Elisabeth ;

Dzubiella, Joachim ;

Rief, Matthias ;

Forest, Katrina T. .

BIOPHYSICAL JOURNAL, 2009, 96 (04) :1508-1514

[7] Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil [J].

Burban, David J. ;

Haglund, Ellinor ;

Capraro, Dominique T. ;

Jennings, Patricia A. .

JOURNAL OF PHYSICS-CONDENSED MATTER, 2015, 27 (35)

[8] Untangling the Influence of a Protein Knot on Folding [J].

Capraro, Dominique T. ;

Jennings, Patricia A. .

BIOPHYSICAL JOURNAL, 2016, 110 (05) :1044-1051

[9] Cotranslational folding of deeply knotted proteins [J].

Chwastyk, Mateusz ;

Cieplak, Marek .

JOURNAL OF PHYSICS-CONDENSED MATTER, 2015, 27 (35)

[10] Multiple folding pathways of proteins with shallow knots and co-translational folding [J].

Chwastyk, Mateusz ;

Cieplak, Marek .

JOURNAL OF CHEMICAL PHYSICS, 2015, 143 (04)

← 1 2 3 4 5 6 7 →