scholarly journals Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway

2020 ◽  
Vol 432 (21) ◽  
pp. 5765-5783
Author(s):  
Richa Gupta ◽  
Yong Liu ◽  
Huanchen Wang ◽  
Christopher T. Nordyke ◽  
Ryan Z. Puterbaugh ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Cgmp Phosphodiesterase ◽  
Allosteric Communication ◽  
Communication Pathway

scholarly journals Mechanistic insights into the active site and allosteric communication pathways in human nonmuscle myosin-2C

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Krishna Chinthalapudi ◽  
Sarah M Heissler ◽  
Matthias Preller ◽  
James R Sellers ◽  
Dietmar J Manstein
Keyword(s):  
Active Site ◽  
Structural Changes ◽  
Motor Domain ◽  
Dynamics Simulation ◽  
Actin Binding ◽  
Nonmuscle Myosin ◽  
Cortical Actin ◽  
Allosteric Communication ◽  
Myosin Motor Domain ◽  
Communication Pathway

Despite a generic, highly conserved motor domain, ATP turnover kinetics and their activation by F-actin vary greatly between myosin-2 isoforms. Here, we present a 2.25 Å pre-powerstroke state (ADP⋅VO4) crystal structure of the human nonmuscle myosin-2C motor domain, one of the slowest myosins characterized. In combination with integrated mutagenesis, ensemble-solution kinetics, and molecular dynamics simulation approaches, the structure reveals an allosteric communication pathway that connects the distal end of the motor domain with the active site. Disruption of this pathway by mutation of hub residue R788, which forms the center of a cluster of interactions connecting the converter, the SH1-SH2 helix, the relay helix, and the lever, abolishes nonmuscle myosin-2 specific kinetic signatures. Our results provide insights into structural changes in the myosin motor domain that are triggered upon F-actin binding and contribute critically to the mechanochemical behavior of stress fibers, actin arcs, and cortical actin-based structures.

scholarly journals A Mammalian Actin Substitution in Yeast Actin (H372R) Causes a Suppressible Mitochondria/Vacuole Phenotype

2005 ◽  
Vol 280 (43) ◽  
pp. 36494-36501 ◽  
Author(s):  
Melissa McKane ◽  
Kuo-Kuang Wen ◽  
Istvan R. Boldogh ◽  
Sharmilee Ramcharan ◽  
Liza A. Pon ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Skeletal Muscle ◽  
Structural Analysis ◽  
Sole Carbon Source ◽  
Actin Polymerization ◽  
Muscle Actin ◽  
Actin Monomer ◽  
Wild Type ◽  
Allosteric Communication ◽  
Related Proteins

To determine the reason for the inviability of Saccharomyces cerevisiae with skeletal muscle actin, we introduced into yeast actin the first variant muscle residue from the C-terminal end, H372R. Arg is also found at this position in non-yeast nonmuscle actins. The substitution caused retarded growth on glucose and an inability to use glycerol as a sole carbon source. The mitochondria were clumped and had lost their DNA, the vacuole appeared hypervesiculated, and the actin cytoskeleton became somewhat depolarized. Introduction of the second muscle actin-specific substitution, S365A, rescued these defects. Suppression was also achieved by introducing the four acidic N-terminal residues of muscle actin in place of the two found in yeast actin. The H372R substitution results in an increase in polymerization-dependent fluorescence of Cys-374 pyrene-labeled actin. H372R actin polymerizes slightly faster than wild-type (WT) actin. Yeast actin-related proteins 2 and 3 (Arp2/3) accelerates the polymerization of H372R actin to a much greater extent than WT actin. The two suppressors did not affect the rate of H372R actin polymerization in the absence of an Arp2/3 complex. In contrast, the S365A substitution dampened the rate of Arp2/3 complex-stimulated H372R actin polymerization, and the addition of the four acidic N-terminal residues caused this rate to decrease below that observed with WT actin in the presence of Arp2/3. Structural analysis of the mutations suggests the presence of stringent steric and ionic requirements for the bottom of actin subdomain 1 and also suggests that there is allosteric communication through subdomain 1 within the actin monomer between the N and C termini.

scholarly journals Chromokinesins NOD and KID Use Distinct ATPase Mechanisms and Microtubule Interactions to Perform a Similar Function

2019 ◽  
Author(s):  
Benjamin C. Walker ◽  
Wolfram Tempel ◽  
Haizhong Zhu ◽  
Heewon Park ◽  
Jared C. Cochran
Keyword(s):  
Cell Division ◽  
Bound States ◽  
Catalytic Domain ◽  
Atp Hydrolysis ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Domain Structures ◽  
Allosteric Communication ◽  
Conventional Kinesin ◽  
Communication Pathway

Chromokinesins NOD and KID have similar DNA binding domains and functions during cell division, while their motor domain sequences show significant variations. It has been unclear whether these motors have similar structure, chemistry, and microtubule interactions necessary to follow a similar mechanism of force mediation. We used biochemical rate measurements, cosedimentation, and structural analysis to investigate the ATPase mechanisms of the NOD and KID core domains. These experiments and analysis revealed that NOD and KID have different ATPase mechanisms, microtubule interactions, and catalytic domain structures. The ATPase cycles of NOD and KID have different rate limiting steps. The ATPase rate of NOD was robustly stimulated by microtubules albeit its microtubule affinity was weakened in all nucleotide bound states. KID bound microtubules tightly in all nucleotide states and remained associated with the microtubule for more than 100 cycles of ATP hydrolysis before dissociating. The structure of KID was most similar to conventional kinesin (KIF5). Key differences in the microtubule binding region and allosteric communication pathway between KID and NOD are consistent with our biochemical data. Our results support the model that NOD and KID utilize distinct mechanistic pathways to achieve the same function during cell division.

scholarly journals Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor

2020 ◽  
Vol 6 (29) ◽  
pp. eabb5277 ◽  
Author(s):  
C. Köhler ◽  
G. Carlström ◽  
A. Gunnarsson ◽  
U. Weininger ◽  
S. Tångefjord ◽  
...  
Keyword(s):  
Communication Network ◽  
Glucocorticoid Receptor ◽  
Transcriptional Activation ◽  
Binding Pocket ◽  
Activation Function ◽  
Allosteric Control ◽  
Allosteric Communication ◽  
Helix 12 ◽  
Transmission Pathways ◽  
Communication Pathway

Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.

The Conserved A-site Finger of the 23S rRNA: Just One of the Intersubunit Bridges or a Part of the Allosteric Communication Pathway?

2005 ◽  
Vol 353 (1) ◽  
pp. 116-123 ◽  
Author(s):  
Petr V. Sergiev ◽  
Sergey V. Kiparisov ◽  
Dmitry E. Burakovsky ◽  
Dmitry V. Lesnyak ◽  
Andrei A. Leonov ◽  
...  
Keyword(s):  
23S Rrna ◽  
Allosteric Communication ◽  
A Site ◽  
Communication Pathway

scholarly journals Mechanistic Insights into the Active Site and Allosteric Communication Pathways in Human Nonmuscle Myosin-2C

2017 ◽  
Author(s):  
Krishna Chinthalapudi ◽  
Sarah M. Heissler ◽  
Matthias Preller ◽  
James R. Sellers ◽  
Dietmar J. Manstein
Keyword(s):  
Active Site ◽  
Structural Changes ◽  
Release Kinetics ◽  
Motor Domain ◽  
Actin Binding ◽  
Nonmuscle Myosin ◽  
Cortical Actin ◽  
Allosteric Communication ◽  
Dynamics Simulations ◽  
Communication Pathway

AbstractThe cyclical interaction of myosin with F-actin and nucleotides is the basis for contractility of the actin cytoskeleton. Despite a generic, highly conserved motor domain, ATP turnover kinetics and their activation by F-actin vary greatly between myosins-2 isoforms. Here, we present a 2.25 Å crystal structure of the human nonmuscle myosin-2C motor domain, one of the slowest myosins characterized. In combination with integrated mutagenesis, ensemble-solution kinetics, and molecular dynamics simulations approaches, this study reveals an allosteric communication pathway that connects the distal end of the motor domain with the active site. Genetic disruption of this pathways reduces nucleotide binding and release kinetics up to 85-fold and abolishes nonmuscle myosin-2 specific kinetic signatures. These results provide insights into structural changes in the myosin motor domain that are triggered upon F-actin binding and contribute critically to the mechanochemical behavior of stress fibers, actin arcs, and cortical actin-based structures.

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