Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Sunitha, Margaret S.; Nair, Archana Padmanabhan; Charya, Amol; Jadhav, Kamalakar; Mukhopadhyay, Sudipta; Sowdhamini, Ramanathan

doi:10.1186/1756-0500-5-530

Cited by 15 publications

(22 citation statements)

References 60 publications

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“…Thus, the conserved sequence of the coiled‐coil domain is confined within a fragment with exact length, since both helices are precisely 54 amino acids long. In general, conservation of the size of a protein domain is higher for coiled‐coil domains than for non‐coiled‐coil fragments (e.g., helices) and is independent of amino acid sequence variation . These data lead to the hypothesis that the conserved length of the coiled‐coil domain in sGC is a key factor in signal transduction and directly linked to sGC function.…”

Section: Resultsmentioning

confidence: 99%

Instability in a coiled‐coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase

et al. 2019

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How nitric oxide (NO) activates its primary receptor, α1/β1 soluble guanylyl cyclase (sGC or GC‐1), remains unknown. Likewise, how stimulatory compounds enhance sGC activity is poorly understood, hampering development of new treatments for cardiovascular disease. NO binding to ferrous heme near the N‐terminus in sGC activates cyclase activity near the C‐terminus, yielding cGMP production and physiological response. CO binding can also stimulate sGC, but only weakly in the absence of stimulatory small‐molecule compounds, which together lead to full activation. How ligand binding enhances catalysis, however, has yet to be discovered. Here, using a truncated version of sGC from Manduca sexta, we demonstrate that the central coiled‐coil domain, the most highly conserved region of the ~150,000 Da protein, not only provides stability to the heterodimer but is also conformationally active in signal transduction. Sequence conservation in the coiled coil includes the expected heptad‐repeating pattern for coiled‐coil motifs, but also invariant positions that disfavor coiled‐coil stability. Full‐length coiled coil dampens CO affinity for heme, while shortening of the coiled coil leads to enhanced CO binding. Introducing double mutation αE447L/βE377L, predicted to replace two destabilizing glutamates with leucines, lowers CO binding affinity while increasing overall protein stability. Likewise, introduction of a disulfide bond into the coiled coil results in reduced CO affinity. Taken together, we demonstrate that the heme domain is greatly influenced by coiled‐coil conformation, suggesting communication between heme and catalytic domains is through the coiled coil. Highly conserved structural imperfections in the coiled coil provide needed flexibility for signal transduction.

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Section: Resultsmentioning

confidence: 99%

Instability in a coiled‐coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase

et al. 2019

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“…To model the effects of TNNT2 mutations, we introduced them into the model to detect possible changes in interactions and interface energy between TNT1 and Tm. The mutations were introduced using SYBYL software, and the interface energies were calculated using COILCHECK+ (34). The positions of pathogenic substitutions on the model are shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region

Gangadharan

Sunitha

Mukherjee

et al. 2017

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

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Point mutations in genes encoding sarcomeric proteins are the leading cause of inherited primary cardiomyopathies. Among them are mutations in the gene that encodes cardiac troponin T (TnT). These mutations are clustered in the tropomyosin (Tm) binding region of TnT, TNT1 (residues 80-180). To understand the mechanistic changes caused by pathogenic mutations in the TNT1 region, six hypertrophic cardiomyopathy (HCM) and two dilated cardiomyopathy (DCM) mutants were studied by biochemical approaches. Binding assays in the absence and presence of actin revealed changes in the affinity of some, but not all, TnT mutants for Tm relative to WT TnT. HCM mutants were hypersensitive and DCM mutants were hyposensitive to Ca in regulated actomyosin ATPase activities. To gain better insight into the disease mechanism, we modeled the structure of TNT1 and its interactions with Tm. The stability predictions made by the model correlated well with the affinity changes observed in vitro of TnT mutants for Tm. The changes in Ca sensitivity showed a strong correlation with the changes in binding affinity. We suggest the primary reason by which these mutations between residues 92 and 144 cause cardiomyopathy is by changing the affinity of TnT for Tm within the TNT1 region.

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“…However, the (i, i ϩ 4) (i.e. (EAAAK) 3 ) spacing yielded significantly higher helicity when compared with (i, i ϩ 3), presumably due to the preferred rotamer configurations of the Glu and Lys side chains. Interestingly, the measured helicity was preserved at extremes of pH (from 2 to 12) and at high concentrations of NaCl, suggesting that the electrostatic interactions were primarily derived from salt bridges (H-bonded ionic interactions) rather than direct ionic interactions.…”

Section: Stable Synthetic Alanine-based ␣-Helicesmentioning

confidence: 99%

“…As the heptad is repeated, it forms a continuous hydrophobic patch located along a single face of the ␣-helix compatible with a tight intermolecular interaction between polypeptides with the same or similar heptad pattern (2). However, often polar or charged residues occupy the a and d positions, leading to local destabilization of the coiled-coil motif (2)(3)(4). By extension, when most or all of the a and d sites in consecutive heptads are occupied by polar residues, individual ␣-helices cannot be mutually stabilized through hydrophobic packing.…”

Section: Coiled-coil or Single ␣-Helical (Sah) Domain?mentioning

confidence: 99%

Harnessing the Unique Structural Properties of Isolated α-Helices

Swanson

Sivaramakrishnan

2014

Journal of Biological Chemistry

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The ␣-helix is a ubiquitous secondary structural element that is almost exclusively observed in proteins when stabilized by tertiary or quaternary interactions. However, beginning with the unexpected observations of ␣-helix formation in the isolated C-peptide in ribonuclease A, there is growing evidence that a significant percentage (0.2%) of all proteins contain isolated stable single ␣-helical domains (SAH). These SAH domains provide unique structural features essential for normal protein function. A subset of SAH domains contain a characteristic ER/K motif, composed of a repeating sequence of ϳ4 consecutive glutamic acids followed by ϳ4 consecutive basic arginine or lysine (R/K) residues. The ER/K ␣-helix, also termed the ER/K linker, has been extensively characterized in the context of the myosin family of molecular motors and is emerging as a versatile structural element for protein and cellular engineering applications. Here, we review the structure and function of SAH domains, as well as the tools to identify them in natural proteins. We conclude with a discussion of recent studies that have successfully used the modular ER/K linker for engineering chimeric myosin proteins with altered mechanical properties, as well as synthetic polypeptides that can be used to monitor and systematically modulate protein interactions within cells. Coiled-coil or Single ␣-Helical (SAH) Domain?Until recently, SAH 2 domains in natural proteins were predicted by secondary structure prediction algorithms to form a coiled-coil, in part due to the high concentration of charged and polar residues that are also the hallmark of the coiled-coil motif (1). Among the multiple folds in globular proteins that stabilize ␣-helices, the coiled-coil motif has been extensively characterized and in general is the most predictable form of tertiary protein structure (2). In the coiled-coil motif, two or more ␣-helices are individually stabilized by sequence-specific packing at consensus hydrophobic patches. Extensive studies have elicited general sequence and structure rules that govern coiled-coil interactions. Briefly, the amino acid sequence of each ␣-helix in a coiled-coil is divided into heptads (7 residues) that form nearly two complete ␣-helical turns and span 1.05 nm along the helical axis. Each amino acid in the heptad is described by its relative position, moving from the N to C terminus, using the nomenclature abcdefg. In canonical dimeric coiled-coils, the a and d positions radiate away from the core of the ␣-helix, 60°a part and offset by 0.45 nm along the helix length, and are typically occupied by aliphatic hydrophobic residues, whereas polar residues comprise the rest of the positions. As the heptad is repeated, it forms a continuous hydrophobic patch located along a single face of the ␣-helix compatible with a tight intermolecular interaction between polypeptides with the same or similar heptad pattern (2). However, often polar or charged residues occupy the a and d positions, leading to local destabilization of the coiled-coil...

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Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Cited by 15 publications

References 60 publications

Instability in a coiled‐coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase

Instability in a coiled‐coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase

Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region

Harnessing the Unique Structural Properties of Isolated α-Helices

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