Effects of nucleotide binding on thermal transitions and domain structure of myosin subfragment 1

Levitsky, Dmitrii I.; Shnyrov, Valery L.; Khvorov, Nikolai V.; Bukatina, Anna E.; Vedenkina, Natalia S.; Permyakov, Eugene A.; Nikolaeva, Olga; Poglazov, B. F.

doi:10.1111/j.1432-1033.1992.tb17354.x

Cited by 54 publications

(77 citation statements)

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“…This effect is very similar to the effect found earlier for the formation of Sl . ADP * Vi complex [6] (data not shown).…”

Section: Methodsmentioning

confidence: 99%

“…Calorimetric measurements were carried out on a differential adiabatic scanning microcalorimeter DASM-4 (Russia) as described earlier [6]. All the measurements were carried out in 30 mM HEPES, pH 7.3, containing 1 mM MgC12 at protein concentration 1 mg/ml and a constant heating rate l"C/min.…”

Section: Methodsmentioning

confidence: 99%

“…All the measurements were carried out in 30 mM HEPES, pH 7.3, containing 1 mM MgC12 at protein concentration 1 mg/ml and a constant heating rate l"C/min. Decomposition of the total heat sorp-tion curves into elementary peaks was performed by the 'successive annealing' method as described earlier [6]. The denaturation enthalpy, AH, was calculated as described by Privalov et al [lo].…”

Section: Methodsmentioning

confidence: 99%

“…It has been shown that the trapping of ADP by Vi in the active site of Sl causes the global change of S 1 conformation which is reflected in a pronounced increase of Sl thermal stability and in a significant change of Sl domain structure [6]. Thus, this method allows to register the conformational changes of the whole Sl molecule caused by formation of the Sl .…”

Section: Introductionmentioning

confidence: 99%

“…Recently we have studied the thermal denaturation of S 1 in the S 1 * ADP * Vi complex by means of differential scanning microcalorimetry [6]. It has been shown that the trapping of ADP by Vi in the active site of Sl causes the global change of S 1 conformation which is reflected in a pronounced increase of Sl thermal stability and in a significant change of Sl domain structure [6].…”

Section: Introductionmentioning

confidence: 99%

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Calorimetric characterization of the stable complex of myosin subfragment 1 with ADP and beryllium fluoride

et al. 1993

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The thermal unfolding of the myosin subfragment 1 (Sl) in its stable complex with ADP and beryllium fluoride (Sl . ADP . BeF;) was studied by differential scanning calorimetry. It has been shown that the structure of the Sl molecule in the Sl ADP . BeF; complex is similar to that of Sl in its complex with ADP and orthovanadate (Sl ADP . Vi) but differs radically from that of nucleotide-free Sl and Sl in the Sl . ADP complex. It is concluded that the Sl . ADP . BeF; complex can be considered, like the Sl . ADP . Vi complex, a stable structural analogue of the myosin head ADP Pi transition state of the myosin-catalyzed ATP hydrolysis.

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“…This effect is very similar to the effect found earlier for the formation of Sl . ADP * Vi complex [6] (data not shown).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Calorimetric characterization of the stable complex of myosin subfragment 1 with ADP and beryllium fluoride

et al. 1993

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Physical driving force of actomyosin motility based on the hydration effect

et al. 2017

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We propose a driving force hypothesis based on previous thermodynamics, kinetics and structural data as well as additional experiments and calculations presented here on water-related phenomena in the actomyosin systems. Although Szent-Györgyi pointed out the importance of water in muscle contraction in 1951, few studies have focused on the water science of muscle because of the difficulty of analyzing hydration properties of the muscle proteins, actin, and myosin. The thermodynamics and energetics of muscle contraction are linked to the water-mediated regulation of protein-ligand and protein-protein interactions along with structural changes in protein molecules. In this study, we assume the following two points: (1) the periodic electric field distribution along an actin filament (F-actin) is unidirectionally modified upon binding of myosin subfragment 1 (M or myosin S1) with ADP and inorganic phosphate Pi (M.ADP.Pi complex) and (2) the solvation free energy of myosin S1 depends on the external electric field strength and the solvation free energy of myosin S1 in close proximity to F-actin can become the potential force to drive myosin S1 along F-actin. The first assumption is supported by integration of experimental reports. The second assumption is supported by model calculations utilizing molecular dynamics (MD) simulation to determine solvation free energies of a small organic molecule and two small proteins. MD simulations utilize the energy representation method (ER) and the roughly proportional relationship between the solvation free energy and the solvent-accessible surface area (SASA) of the protein. The estimated driving force acting on myosin S1 is as high as several piconewtons (pN), which is consistent with the experimentally observed force.

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Characterizing the microenvironment surrounding protein sites

1995

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Sites are microenvironments within a biomolecular structure, distinguished by their structural or functional role. A site can be defined by a three-dimensional location and a local neighborhood around this location in which the structure or function exists. We have developed a computer system to facilitate structural analysis (both qualitative and quantitative) of biomolecular sites. Our system automatically examines the spatial distributions of biophysical and biochemical properties, and reports those regions within a site where the distribution of these properties differs significantly from control nonsites. The properties range from simple atom-based characteristics such as charge to polypeptide-based characteristics such as type of secondary structure. Our analysis of sites uses nonsites as controls, providing a baseline for the quantitative assessment of the significance of the features that are uncovered. In this paper, we use radial distributions of properties to study three well-known sites (the binding sites for calcium, the milieu of disulfide bridges, and the serine protease active site). We demonstrate that the system automatically finds many of the previously described features of these sites and augments these features with some new details. In some cases, we cannot confirm the statistical significance of previously reported features. Our results demonstrate that analysis of protein structure is sensitive to assumptions about background distributions, and that these distributions should be considered explicitly during structural analyses.Keywords: biophysical properties; calcium binding; computational biology; disulfide bridges; microenvironment; protein structure analysis; serine proteases; software Central to molecular biology is the determination of macromolecular structure and the analysis of how structural elements produce an observed function. The principles by which structure relates to function have been elucidated in a piecemeal fashion, from work on single structures or small classes of structures. Computational assistance has come primarily in the form of graphical methods for scientific visualization and from special purpose programs for analyzing individual biophysical properties (such as solvent accessibility or electrostatic fields). Unfortunately, studying structures individually entails a risk of missing important relationships that would be revealed by pooling relevant data. The expected surfeit of protein structures provides an opportunity to develop tools for automatically examining biological structures and producing useful representations of the key biophysical and biochemical features. The utility of a general purpose system for producing these representations would extend from medical/pharmaceutical applications (model-based drug design, comparing pharmacological Reprint requests to: Russ B. Altman, Section on Medical Informatics, Stanford University School of Medicine, MSOB X-215, Stanford, California 94305-5479; e-mail: altman@camis.stanford.edu. activities) to ind...

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Effects of nucleotide binding on thermal transitions and domain structure of myosin subfragment 1

Cited by 54 publications

References 50 publications

Calorimetric characterization of the stable complex of myosin subfragment 1 with ADP and beryllium fluoride

Calorimetric characterization of the stable complex of myosin subfragment 1 with ADP and beryllium fluoride

Physical driving force of actomyosin motility based on the hydration effect

Characterizing the microenvironment surrounding protein sites

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