2017
DOI: 10.1073/pnas.1621344114
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Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Abstract: We recently introduced a physically based approach to sequence comparison, the property factor method (PFM). In the present work, we apply the PFM approach to the study of a challenging set of sequences-the bacterial chemotaxis protein CheY, the N-terminal receiver domain of the nitrogen regulation protein NT-NtrC, and the sporulation response regulator Spo0F. These are all response regulators involved in signal transduction. Despite functional similarity and structural homology, they exhibit low sequence iden… Show more

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Cited by 32 publications
(23 citation statements)
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“…To investigate in detail the structural alterations after zinc binding, we compared the MD simulation trajectories of apo-AdcA, Zn-N-AdcA, and Zn 2 -AdcA. The mean distance matrix showed remarkably decreased interdomain distances when the N-terminal domain bound a zinc atom (29) (Fig. 5A), which can be visualized in the steady-state three-dimensional conformations ( Fig.…”
Section: Structural Alteration Upon Zinc Bindingmentioning
confidence: 99%
“…To investigate in detail the structural alterations after zinc binding, we compared the MD simulation trajectories of apo-AdcA, Zn-N-AdcA, and Zn 2 -AdcA. The mean distance matrix showed remarkably decreased interdomain distances when the N-terminal domain bound a zinc atom (29) (Fig. 5A), which can be visualized in the steady-state three-dimensional conformations ( Fig.…”
Section: Structural Alteration Upon Zinc Bindingmentioning
confidence: 99%
“…Proteins are the molecules in the cell that carry out the activities encoded by genes. They are the group of enzymes responsible for catalyzing a wide range of intracellular and extracellular chemical reactions [24]. Therefore, proteins are grouped into specialized classes based on their importance.…”
Section: Relationship Between Protein Structure and Its Functionsmentioning
confidence: 99%
“…Structural proteins are, at their simplest, assemblages of single type of protein molecules bound together for strength or toughness. In more complex cases they bind to other types of molecules to form specialized structures such as the actin-based intestinal microvilli or the spectrin-based mesh that underlies the red blood cell membrane and helps maintain its integrity as the cells are swept round the body [8,24]. Protein switches such as the GTPases depend on both binding and catalytic functions of proteins.…”
Section: Binding Proteinsmentioning
confidence: 99%
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