Binding of bisubstrate analog promotes large structural changes in the unregulated catalytic trimer of aspartate transcarbamoylase: Implications for allosteric regulation

2006 ◽  
Vol 17 (1-2) ◽  
pp. 133-145
Author(s):  
Tom Alber ◽  
James A. Endrizzi ◽  
Howard K. Schachman ◽  
Peter T. Beernink
Keyword(s):  
Structural Changes ◽  
Allosteric Regulation ◽  
Aspartate Transcarbamoylase

An ensemble view of thrombin allostery

2012 ◽  
Vol 393 (9) ◽  
pp. 889-898 ◽  
Author(s):  
Bernhard C. Lechtenberg ◽  
Stefan M.V. Freund ◽  
James A. Huntington
Keyword(s):  
Structural Changes ◽  
Allosteric Regulation ◽  
Monovalent Cation ◽  
Coagulation Cascade ◽  
General View ◽  
Multiple Substrates ◽  
Dynamic View ◽  
Static View ◽  
Two State Model ◽  
The Continuum

Abstract Thrombin is the central protease of the coagulation cascade. Its activity is tightly regulated to ensure rapid blood clotting while preventing uncontrolled thrombosis. Thrombin interacts with multiple substrates and cofactors and is critically involved in both pro- and anticoagulant pathways of the coagulation network. Its allosteric regulation, especially by the monovalent cation Na+, has been the focus of research for more than 30 years. It is believed that thrombin can adopt an anticoagulant (‘slow’) conformation and, after Na+ binding, a structurally distinct procoagulant (‘fast’) state. In the past few years, however, the general view of allostery has evolved from one of rigid structural changes towards thermodynamic ensembles of conformational states. With this background, the view of the allosteric regulation of thrombin has also changed. The static view of the two-state model has been dismissed in favor of a more dynamic view of thrombin allostery. Herein, we review recent data that demonstrate that apo-thrombin is zymogen-like and exists as an ensemble of conformations. Furthermore, we describe how ligand binding to thrombin allosterically stabilizes conformations on the continuum from zymogen to protease.

Allosteric regulation of aspartate transcarbamoylase. Analysis of the structural and functional behavior in terms of a two-state model

Biochemistry ◽  
1977 ◽  
Vol 16 (23) ◽  
pp. 5091-5099 ◽  
Author(s):  
G. J. Howlett ◽  
Michael N. Blackburn ◽  
John G. Compton ◽  
H. K. Schachman
Keyword(s):  
Allosteric Regulation ◽  
State Model ◽  
Aspartate Transcarbamoylase ◽  
Functional Behavior ◽  
Two State Model

New Paradigm for Allosteric Regulation of Escherichia coli Aspartate Transcarbamoylase

Biochemistry ◽  
2013 ◽  
Vol 52 (45) ◽  
pp. 8036-8047 ◽  
Author(s):  
Gregory M. Cockrell ◽  
Yunan Zheng ◽  
Wenyue Guo ◽  
Alexis W. Peterson ◽  
Jennifer K. Truong ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Allosteric Regulation ◽  
Aspartate Transcarbamoylase ◽  
New Paradigm

scholarly journals Allosteric Regulation of Catalytic Activity:Escherichia coli Aspartate Transcarbamoylase versus Yeast Chorismate Mutase

2001 ◽  
Vol 65 (3) ◽  
pp. 404-421 ◽  
Author(s):  
Kerstin Helmstaedt ◽  
Sven Krappmann ◽  
Gerhard H. Braus
Keyword(s):  
Conformational Changes ◽  
Classical Model ◽  
Allosteric Regulation ◽  
Chorismate Mutase ◽  
Aspartate Transcarbamoylase ◽  
Detailed Knowledge ◽  
Wild Type ◽  
Function Relationship ◽  
Relationship Of ◽  
Entire Picture

SUMMARY Allosteric regulation of key metabolic enzymes is a fascinating field to study the structure-function relationship of induced conformational changes of proteins. In this review we compare the principles of allosteric transitions of the complex classical model aspartate transcarbamoylase (ATCase) from Escherichia coli, consisting of 12 polypeptides, and the less complicated chorismate mutase derived from baker's yeast, which functions as a homodimer. Chorismate mutase presumably represents the minimal oligomerization state of a cooperative enzyme which still can be either activated or inhibited by different heterotropic effectors. Detailed knowledge of the number of possible quaternary states and a description of molecular triggers for conformational changes of model enzymes such as ATCase and chorismate mutase shed more and more light on allostery as an important regulatory mechanism of any living cell. The comparison of wild-type and engineered mutant enzymes reveals that current textbook models for regulation do not cover the entire picture needed to describe the function of these enzymes in detail.

scholarly journals Distinct binding modes and structural changes induced by cAMP and cGMP in the GAF domain of Anabaena adenylyl cyclase, CyaB2

2014 ◽  
Author(s):  
Kabir H Biswas ◽  
Suguna Badireddy ◽  
Ganesh S Anand ◽  
Sandhya S Visweswariah
Keyword(s):  
Ligand Binding ◽  
Adenylyl Cyclase ◽  
Structural Changes ◽  
Mutational Analysis ◽  
Allosteric Regulation ◽  
Large Family ◽  
Structural Basis ◽  
Binding Modes ◽  
Cyclase Domain ◽  
Camp And Cgmp

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem (GAFab domain). In silico docking and mutational analysis indicated distinct modes of binding of cAMP and cGMP to the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by the highly sensitive Bioluminescence Resonance Energy Transfer (BRET) experiments. Amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments, however, revealed the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the structural changes induced by cAMP and cGMP binding to the GAF domain. Thus, our results provide an insight into structural mechanisms of ligand binding to GAF domains in general, which can be utilized in developing molecules that modulate the allosteric regulation by GAF domains in pharmacologically relevant proteins.

scholarly journals Distinct binding modes and structural changes induced by cAMP and cGMP in the GAF domain of Anabaena adenylyl cyclase, CyaB2

2014 ◽  
Author(s):  
Kabir H Biswas ◽  
Suguna Badireddy ◽  
Ganesh S Anand ◽  
Sandhya S Visweswariah
Keyword(s):  
Ligand Binding ◽  
Adenylyl Cyclase ◽  
Structural Changes ◽  
Mutational Analysis ◽  
Allosteric Regulation ◽  
Large Family ◽  
Structural Basis ◽  
Binding Modes ◽  
Cyclase Domain ◽  
Camp And Cgmp

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem (GAFab domain). In silico docking and mutational analysis indicated distinct modes of binding of cAMP and cGMP to the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by the highly sensitive Bioluminescence Resonance Energy Transfer (BRET) experiments. Amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments, however, revealed the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the structural changes induced by cAMP and cGMP binding to the GAF domain. Thus, our results provide an insight into structural mechanisms of ligand binding to GAF domains in general, which can be utilized in developing molecules that modulate the allosteric regulation by GAF domains in pharmacologically relevant proteins.

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