Multiple Time Scale Backbone Dynamics of Homologous Thermophilic and Mesophilic Ribonuclease HI Enzymes

Butterwick, Joel A.; Loria, J. Patrick; Astrof, Nathan S.; Kroenke, Christopher D.; Cole, R D; Rance, Mark; Palmer, Arthur G.

doi:10.1016/j.jmb.2004.03.055

Cited by 76 publications

(130 citation statements)

References 85 publications

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“…The current study represents one of the very few experimental validations of similar conformational exchange in structurally related enzymes (26,27) and the first to compare similar mesophile homologues, confirming theoretical observations suggesting that specific motions can be evolutionarily conserved within and among structurally similar protein folds. The present work also demonstrates the importance of controlling millisecond dynamics to modulate protein function, a central concept with broad implications in protein engineering and allosteric drug design (4,5,28,29).…”

supporting

confidence: 82%

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Gagné

Charest

Morin

et al. 2012

Journal of Biological Chemistry

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Background: It remains unclear whether structural homologues rely on similar concerted motions to promote enzyme function. Results: Ribonuclease homologues display similar, contiguous clustering motions that can be modulated by mutagenesis. Conclusion: Conformational flexibility can be conserved between distant structural homologues. Significance: Controlling dynamics to modulate function has broad implications in protein engineering and allosteric drug design.

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supporting

confidence: 82%

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Gagné

Charest

Morin

et al. 2012

Journal of Biological Chemistry

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“…As lower temperature increases rigidity, the Pab PolII intein is expected to be much more rigid than the Mtu RecA intein at 25°C. In contrast, similar order parameters were found in E. coli and Thermus thermophilus ribonuclease H (55). This enhanced rigidity may prevent the Pab PolII intein from sampling active conformations important for protein splicing at low temperatures.…”

Section: Journal Of Biological Chemistrymentioning

confidence: 60%

Structural and Mutational Studies of a Hyperthermophilic Intein from DNA Polymerase II of Pyrococcus abyssi

Liu

Albracht

et al. 2011

Journal of Biological Chemistry

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Background:The PolII intein from the hyperthermophilic Pyrococcus abysii only splices at very high temperature. Results: NMR structure, dynamics, and mutagenesis of Pab PolII intein have been characterized. Conclusion:The Pab PolII intein has unique structural and dynamic features that may contribute to its higher temperature for optimal activity. Significance: Pab PolII intein is an ideal candidate for protein engineering.

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“…Thus, it seems that high activity does not have to be related to low stability and can accompany high stability by adjusting the flexibility of regions that are less important for stability. Uncoupling between global flexibility and stability also has been suggested in other systems using different experimental techniques such as NMR relaxation (16) and H͞D exchange (17).…”

Section: Discussionmentioning

confidence: 99%

“…Clues to connections between amino acid sequence, structure, dynamics, and catalysis can be obtained by comparing and contrasting highly similar proteins from psychrophiles, mesophiles, and thermophiles (15)(16)(17). We have previously reported crystal structures, thermal stabilities, and temperature activity profiles for three such proteins from the genus Bacillus (18).…”

mentioning

confidence: 99%

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

Bae

Phillips

2006

Proc. Natl. Acad. Sci. U.S.A.

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Protein dynamics, including conformational switching, are recognized to be crucial for the function of many systems. These motions are more challenging to study than simple static structures. Here, we present evidence suggesting that in the enzyme adenylate kinase large ''hinge bending'' motions closely related to catalysis are regulated by intrinsic properties of the moving domains and not by their hinges, by anchoring domains, or by remote allostericlike regions. From a pair of highly homologous mesophilic and thermophilic adenylate kinases, we generated a series of chimeric enzymes using a previously undescribed method with synthetic genes. Subsequent analysis of the chimeras has revealed unexpected spatial separation of stability and activity control. Our results highlight specific contributions of dynamics to catalysis in adenylate kinase. Furthermore, the overall strategy and the specific mutagenesis method used in this study can be generally applied.chimeric protein ͉ protein flexibility ͉ thermostability S tructural biology is moving beyond simple analysis of the average structures of proteins to include dynamic components. Mounting evidence suggests that dynamic motions of proteins play specific and essential roles in function (1-6), but the mechanism is rarely clear. Adenylate kinase (AK) is an excellent target for the study of connections between dynamics and function of protein. It is a small enzyme catalyzing reversible conversions between ATP͞AMP and two ADP molecules (7). Structures have been solved of various states of the enzyme from various organisms and revealed a large conformational rearrangement of the enzyme during its catalytic cycle (8, 9). Among the three defined characteristic AK domains CORE, AMP bind , and LID (10), the AMP bind and LID domains are directly involved in the dynamic event and close over the enzyme's AMPand ATP-binding sites, respectively (Fig. 1). A recent NMR experiment suggested that the opening of the AMP bind and͞or LID domains upon product release is the rate-limiting step, with opening times commensurate with the turnover rate (11). It also was proposed that the dynamic motion of AK may involve catastrophic events such as cracking and subsequent reassembly (12, 13). Other than the two mobile domains, two loops in the CORE domain (Fig. 1) displayed substantially increased flexibility upon substrate binding as in allostery and have been suggested to serve as a counterweight balancing the substratebinding energy (9,14).Clues to connections between amino acid sequence, structure, dynamics, and catalysis can be obtained by comparing and contrasting highly similar proteins from psychrophiles, mesophiles, and thermophiles (15-17). We have previously reported crystal structures, thermal stabilities, and temperature activity profiles for three such proteins from the genus Bacillus (18). As might be expected, the catalytic activities and thermal transitions scale with the operating temperatures of the source organisms. There is, however, no a priori reason to expect a dire...

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Multiple Time Scale Backbone Dynamics of Homologous Thermophilic and Mesophilic Ribonuclease HI Enzymes

Cited by 76 publications

References 85 publications

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Conservation of Flexible Residue Clusters among Structural and Functional Enzyme Homologues

Structural and Mutational Studies of a Hyperthermophilic Intein from DNA Polymerase II of Pyrococcus abyssi

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

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