Journal ArticleDOI
Exploring the range of protein flexibility, from a structural proteomics perspective.
Mark Gerstein,Nathaniel Echols +1 more
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TLDR
New data emphasize a breadth of possible structural mechanisms, particularly the ability to drastically alter protein architecture and the native flexibility of many structures, as well as high-resolution studies of increasingly complex assemblies and conformational changes.About:
This article is published in Current Opinion in Chemical Biology.The article was published on 2004-02-01. It has received 73 citations till now. The article focuses on the topics: Flexibility (engineering).read more
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Protein design: toward functional metalloenzymes.
Fangting Yu,Virginia M. Cangelosi,Melissa L. Zastrow,Matteo Tegoni,Jefferson S. Plegaria,Alison G. Tebo,Catherine S. Mocny,Leela Ruckthong,Hira Qayyum,Vincent L. Pecoraro +9 more
TL;DR: De Novo Designed Functional Metalloproteins: The Grail Quest of Protein Design AX 3.2.1.
Journal ArticleDOI
The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.
Elena Papaleo,Giorgio Saladino,Matteo Lambrughi,Kresten Lindorff-Larsen,Francesco Luigi Gervasio,Ruth Nussinov +5 more
TL;DR: A detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties are provided.
Journal ArticleDOI
HingeProt: automated prediction of hinges in protein structures.
Ugur Emekli,Dina Schneidman-Duhovny,Haim J. Wolfson,Ruth Nussinov,Ruth Nussinov,Turkan Haliloglu +5 more
TL;DR: The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins, and can be used in applications such as flexible protein–protein and protein–ligand docking, flexible docking of protein structures into cryo‐EM maps, and refinement of low‐resolution EM structures.
Journal ArticleDOI
Metal Binding Affinity and Selectivity in Metalloproteins: Insights from Computational Studies
Todor Dudev,Carmay Lim +1 more
TL;DR: The results herein reveal the fundamental principles and the molecular bases underlying protein-metal recognition, which serve as a guide to engineer novel metalloproteins with programmed properties.
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Structural basis of gating by the outer membrane transporter FecA
Andrew D. Ferguson,Ranjan Chakraborty,Barbara S. Smith,Lothar Esser,D. Van Der Helm,Johann Deisenhofer +5 more
TL;DR: The crystallographic structure of the integral outer membrane receptor FecA from Escherichia coli with and without ferric citrate is presented, establishing the structural basis of gating for receptors dependent on the cytoplasmic membrane protein TonB.
References
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Journal ArticleDOI
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Axel T. Brunger,Axel T. Brunger,Paul D. Adams,G M Clore,W. L. DeLano,Piet Gros,R.W. Grosse-Kunstleve,R.W. Grosse-Kunstleve,Jiansheng Jiang,J. Kuszewski,Michael Nilges,Navraj S. Pannu,Randy J. Read,Luke M. Rice,Thomas Simonson,Gregory L. Warren +15 more
TL;DR: The Crystallography & NMR System (CNS) as mentioned in this paper is a software suite for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy.
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Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution
TL;DR: Comparison with a low-resolution electron density map of the enzyme in the absence of calcium and with biochemical data suggests that large domain movements take place during active transport.
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The open pore conformation of potassium channels.
TL;DR: Amino-acid sequence conservation suggests a common structural basis for gating in a wide range of K+ channels, both ligand- and voltage-gated.
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Structural changes in the calcium pump accompanying the dissociation of calcium
Chikashi Toyoshima,Hiromi Nomura +1 more
TL;DR: The structure of the enzyme stabilized by thapsigargin, a potent inhibitor, shows large conformation differences from that in E1Ca2+.
Journal ArticleDOI
The principle of gating charge movement in a voltage-dependent K + channel
TL;DR: It is concluded that the voltage-sensor paddles operate somewhat like hydrophobic cations attached to levers, enabling the membrane electric field to open and close the pore.