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Jan Kubelka - One of the best experts on this subject based on the ideXlab platform.
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sequence structure and cooperativity in folding of elementary Protein Structural Motifs
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Jason K Lai, Ginka S Kubelka, Jan KubelkaAbstract:Residue-level unfolding of two helix-turn-helix Proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local Structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saito–Munoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model Proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each Protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two Motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
Jason K Lai - One of the best experts on this subject based on the ideXlab platform.
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sequence structure and cooperativity in folding of elementary Protein Structural Motifs
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Jason K Lai, Ginka S Kubelka, Jan KubelkaAbstract:Residue-level unfolding of two helix-turn-helix Proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local Structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saito–Munoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model Proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each Protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two Motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
Sean Munro - One of the best experts on this subject based on the ideXlab platform.
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the golgin coiled coil Proteins of the golgi apparatus
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Sean MunroAbstract:Coiled-coils are widely occurring Protein Structural Motifs in which two or more α-helices wind around each other to form an extended rod-like structure. Proteins containing such structures are found in many parts of the cell, and play diverse roles including organizing centrosomes, chromatin, and synapses, or serving as molecular motors. As such there may seem little reason to consider them collectively beyond an interest in the Structural and biophysical properties of the coiled-coil itself. However, the Golgi is unique amongst the cellular compartments in that several different large coiled-coil Proteins are present on its cytoplasmic surface (Gillingham and Munro 2003; Lupashin and Sztul 2005; Short et al. 2005; Ramirez and Lowe 2009). A number of these share a similar organization in that most of the Protein is predicted to form a coiled-coil, and that their carboxyl termini mediate attachment to Golgi membranes. They are generally ubiquitously expressed and well conserved in evolution, but their coiled-coil regions are relatively poorly conserved suggesting that much of their length serves as spacer. Given that 500 residues of coiled-coil is ∼75 nm in length then the Proteins could extend for ∼100–400 nm. Some of the Proteins have regions which appear likely to be unstructured and hence could serve as extensions or hinges to increase the Proteins’ reach and flexibility (Oas and Endow 1994; Yamakawa et al. 1996). These shared features suggest that the Proteins serve related functions on the Golgi. The term “golgin” is often applied to these Proteins having been coined in early studies when several were found as human autoantigens (Fritzler et al. 1993), but the term lacks a clear definition. To provide a focus to this article, I will concentrate on “golgins” as defined by being a Protein that is found primarily, if not exclusively, on the Golgi and is predicted to form a homodimeric parallel coiled-coil over most of its length. Proteins with shorter regions of coiled-coil are more likely to have roles distinct to the golgins, especially if further domains are present. Golgin coiled-coil Proteins are found on the cis-face of the Golgi, around the rims of the stack and on the trans-face of the Golgi (Fig. 1). The human golgins are summarized in Table 1, along with their orthologs in model organisms and the rather confusing gene names inflicted by the Human Gene Nomenclature Committee. I discuss what is known about the individual Proteins from each of the parts of the Golgi, and mention briefly the Golgi coiled-coil Proteins that are probably not golgins. I then discuss how the golgins are regulated and how their properties might reflect a shared function in Golgi organization and traffic. Figure 1. The golgin coiled-coil Proteins of humans. Table 1. The canonical golgins of the human Golgi and their orthologs.
Ginka S Kubelka - One of the best experts on this subject based on the ideXlab platform.
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sequence structure and cooperativity in folding of elementary Protein Structural Motifs
Proceedings of the National Academy of Sciences of the United States of America, 2015Co-Authors: Jason K Lai, Ginka S Kubelka, Jan KubelkaAbstract:Residue-level unfolding of two helix-turn-helix Proteins—one naturally occurring and one de novo designed—is reconstructed from multiple sets of site-specific 13C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa–Jernigan statistical potentials), local Structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako–Saito–Munoz–Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model Proteins and their fragments and 13C-amide I′ bands for multiple isotopologues of each Protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two Motifs is different, reflecting the order of local stability. We introduce free energy profiles for “experimental” reaction coordinates—namely, the degree of local folding as sensed by site-specific 13C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
Yongli Zhang - One of the best experts on this subject based on the ideXlab platform.
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highly anisotropic stability and folding kinetics of a single coiled coil Protein under mechanical tension
Journal of the American Chemical Society, 2011Co-Authors: Ying Gao, George Sirinakis, Yongli ZhangAbstract:Coiled coils are one of the most abundant Protein Structural Motifs and widely mediate Protein interactions and force transduction or sensation. They are thus model systems for Protein engineering and folding studies, particularly the GCN4 coiled coil. Major single-molecule methods have also been applied to this Protein and revealed its folding kinetics at various spatiotemporal scales. Nevertheless, the folding energy and kinetics of a single GCN4 coiled coil domain has not been well determined at a single-molecule level. Here we used high-resolution optical tweezers to characterize the folding and unfolding reactions of a single GCN4 coiled coil domain and their dependence on the pulling direction. In one axial and two transverse pulling directions, we observed reversible, two-state transitions of the coiled coil in real time. The transitions equilibrate at pulling forces ranging from 6 to 12 pN, showing different stabilities of the coiled coil in regard to pulling direction. Furthermore, the transition rates vary with both the magnitude and direction of the pulling force by greater than 1,000 folds, indicating a highly anisotropic and topology-dependent energy landscape for Protein transitions under mechanical tension. We developed a new analytical theory to extract energy and kinetics of the Protein transition at zero force. The derived folding energy does not depend on the pulling direction and is consistent with the measurement in bulk, which further confirms the applicability of the single-molecule manipulation approach for energy measurement. The highly anisotropic thermodynamics of Proteins under tension should play important roles in their biological functions.
