scholarly journals Normal‐mode driven exploration of protein domain motions

2021 ◽  
Author(s):  
Yves‐Henri Sanejouand
Keyword(s):  
Normal Mode ◽  
Protein Domain ◽  
Domain Motions

scholarly journals Unusual origins of isotope effects in enzyme-catalysed reactions

2006 ◽  
Vol 361 (1472) ◽  
pp. 1341-1349 ◽  
Author(s):  
Dexter B Northrop
Keyword(s):  
High Pressure ◽  
Isotope Effects ◽  
Heavy Atom ◽  
Zero Point ◽  
Protein Domain ◽  
Enzymatic Reactions ◽  
Volume Changes ◽  
Mass Unit ◽  
Deuterium Isotope Effects ◽  
Domain Motions

High hydrostatic pressure is a neglected tool for probing the origins of isotope effects. In chemical reactions, normal primary deuterium isotope effects (DIEs) arising solely from differences in zero point energies are unaffected by pressure; but some anomalous isotope effects in which hydrogen tunnelling is suspected are partially suppressed. In some enzymatic reactions, high pressure completely suppresses the DIE. We have now measured the effects of high pressure on the parallel 13 C heavy atom isotope effect of yeast alcohol dehydrogenase and found that it is also suppressed by high pressure and, similarly, suppressed in its entirety. Moreover, the volume changes associated with the suppression of both deuterium and heavy atom isotope effects are virtually identical. The equivalent decrease in activation volumes for hydride transfer, when one mass unit is added to the carbon end of a scissile C–H bond as when one mass unit is added to the hydrogen end, suggests a common origin. Given that carbon is highly unlikely to undergo tunnelling, it follows that hydrogen is not doing so either. The origin of these isotope effects must lie elsewhere. We offer protein domain motions as a possibility.

Docking of ATP to Ca-ATPase:  Considering Protein Domain Motions

2007 ◽  
Vol 47 (3) ◽  
pp. 1171-1181 ◽  
Author(s):  
Timothy V. Pyrkov ◽  
Yuri A. Kosinsky ◽  
Alexander S. Arseniev ◽  
John P. Priestle ◽  
Edgar Jacoby ◽  
...  
Keyword(s):  
Protein Domain ◽  
Domain Motions

Observation of Protein Domain Motions by Neutron Spectroscopy

ChemPhysChem ◽  
2010 ◽  
Vol 11 (6) ◽  
pp. 1188-1194 ◽  
Author(s):  
Michael Monkenbusch ◽  
Dieter Richter ◽  
Ralf Biehl
Keyword(s):  
Protein Domain ◽  
Neutron Spectroscopy ◽  
Domain Motions

Domain Motions and the Open-to-Closed Conformational Transition of an Enzyme:  A Normal Mode Analysis ofS-Adenosyl-l-homocysteine Hydrolase†

Biochemistry ◽  
2005 ◽  
Vol 44 (19) ◽  
pp. 7228-7239 ◽  
Author(s):  
Mengmeng Wang ◽  
Ronald T. Borchardt ◽  
Richard L. Schowen ◽  
Krzysztof Kuczera
Keyword(s):  
Normal Mode ◽  
Conformational Transition ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Domain Motions

scholarly journals Clutch mechanism of chemomechanical coupling in a DNA resecting motor nuclease

2021 ◽  
Vol 118 (11) ◽  
pp. e2023955118
Author(s):  
Mihaela-Carmen Unciuleac ◽  
Aviv Meir ◽  
Chaoyou Xue ◽  
Garrett M. Warren ◽  
Eric C. Greene ◽  
...  
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Protein Domain ◽  
Dna Double Strand Breaks ◽  
Dna Translocation ◽  
Strand Breaks ◽  
Chemomechanical Coupling ◽  
Clutch Mechanism ◽  
Dna Strand ◽  
Domain Motions

Mycobacterial AdnAB is a heterodimeric helicase–nuclease that initiates homologous recombination by resecting DNA double-strand breaks (DSBs). The N-terminal motor domain of the AdnB subunit hydrolyzes ATP to drive rapid and processive 3′ to 5′ translocation of AdnAB on the tracking DNA strand. ATP hydrolysis is mechanically productive when oscillating protein domain motions synchronized with the ATPase cycle propel the DNA tracking strand forward by a single-nucleotide step, in what is thought to entail a pawl-and-ratchet–like fashion. By gauging the effects of alanine mutations of the 16 amino acids at the AdnB–DNA interface on DNA-dependent ATP hydrolysis, DNA translocation, and DSB resection in ensemble and single-molecule assays, we gained key insights into which DNA contacts couple ATP hydrolysis to motor activity. The results implicate AdnB Trp325, which intercalates into the tracking strand and stacks on a nucleobase, as the singular essential constituent of the ratchet pawl, without which ATP hydrolysis on ssDNA is mechanically futile. Loss of Thr663 and Thr118 contacts with tracking strand phosphates and of His665 with a nucleobase drastically slows the AdnAB motor during DSB resection. Our findings for AdnAB prompt us to analogize its mechanism to that of an automobile clutch.

scholarly journals An ensemble of flexible conformations underlies mechanotransduction by the cadherin–catenin adhesion complex

2019 ◽  
Vol 116 (43) ◽  
pp. 21545-21555 ◽  
Author(s):  
Martin Bush ◽  
Bashir M. Alhanshali ◽  
Shuo Qian ◽  
Christopher B. Stanley ◽  
William T. Heller ◽  
...  
Keyword(s):  
Small Angle ◽  
Wide Spectrum ◽  
Flexible Structures ◽  
Adherens Junction ◽  
Terminal Segment ◽  
Protein Domain ◽  
Central Component ◽  
Intrinsically Disordered ◽  
Domain Motions ◽  
Adhesion Complex

The cadherin–catenin adhesion complex is the central component of the cell–cell adhesion adherens junctions that transmit mechanical stress from cell to cell. We have determined the nanoscale structure of the adherens junction complex formed by the α-catenin•β-catenin•epithelial cadherin cytoplasmic domain (ABE) using negative stain electron microscopy, small-angle X-ray scattering, and selective deuteration/small-angle neutron scattering. The ABE complex is highly pliable and displays a wide spectrum of flexible structures that are facilitated by protein-domain motions in α- and β-catenin. Moreover, the 107-residue intrinsically disordered N-terminal segment of β-catenin forms a flexible “tongue” that is inserted into α-catenin and participates in the assembly of the ABE complex. The unanticipated ensemble of flexible conformations of the ABE complex suggests a dynamic mechanism for sensitivity and reversibility when transducing mechanical signals, in addition to the catch/slip bond behavior displayed by the ABE complex under mechanical tension. Our results provide mechanistic insight into the structural dynamics for the cadherin–catenin adhesion complex in mechanotransduction.

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