The Experts below are selected from a list of 327 Experts worldwide ranked by ideXlab platform
Jeffrey Skolnick - One of the best experts on this subject based on the ideXlab platform.
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origin of intrinsic 310 helix versus strand stability in homopolypeptides and its implications for the accuracy of the amber force field
Journal of Computational Chemistry, 2007Co-Authors: Anna Jagielska, Jeffrey SkolnickAbstract:Current all-atom force fields often fail to recognize the native Structure of a protein as the lowest free energy minimum. One possible cause could be the mathematical form of the potential based on the assumption that the conformation of a residue is independent of its neighbors. Here, using quantum mechanical (QM) methods (MP2/6-31g**//HF/6-31g** and MP2/cc-pVDZ//cc-pVDZ//HF/cc-pVDZ), the intrinsic correctness of the gas phase terms (without solvation) of the Amber ff03 and ff99 potentials are examined by testing their ability to reproduce the relative 310-helix versus Extended Structure stabilities in the gas phase for 1-7-residue alanine, valine, leucine, and isoleucine homopolypeptides. The 310-helix versus Extended state stability strongly depends on chain length and less on the amino acid identity. The helical conformation becomes lower in energy than the Extended conformation for all tested peptides longer than two residues, and its stability increases with the increase of chain length. The ff03 potential better describes the 310-helix versus Extended state energy than ff99 and also reproduces the curvature of the relative helix-Extended state energies. Therefore, the mathematical form of the Amber potential is sufficient to describe the local effect of 310-helix versus Extended Structure stabilization in the gas phase. However, the energy curves are shifted and the backbone geometries differ compared with the QM results. This may cause significant geometric discrepancies between native and predicted Structures. Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-Extended state energetics and geome- try of major conformations.
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Origin of intrinsic 310‐helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field
Journal of Computational Chemistry, 2007Co-Authors: Anna Jagielska, Jeffrey SkolnickAbstract:Current all-atom force fields often fail to recognize the native Structure of a protein as the lowest free energy minimum. One possible cause could be the mathematical form of the potential based on the assumption that the conformation of a residue is independent of its neighbors. Here, using quantum mechanical (QM) methods (MP2/6-31g**//HF/6-31g** and MP2/cc-pVDZ//cc-pVDZ//HF/cc-pVDZ), the intrinsic correctness of the gas phase terms (without solvation) of the Amber ff03 and ff99 potentials are examined by testing their ability to reproduce the relative 310-helix versus Extended Structure stabilities in the gas phase for 1-7-residue alanine, valine, leucine, and isoleucine homopolypeptides. The 310-helix versus Extended state stability strongly depends on chain length and less on the amino acid identity. The helical conformation becomes lower in energy than the Extended conformation for all tested peptides longer than two residues, and its stability increases with the increase of chain length. The ff03 potential better describes the 310-helix versus Extended state energy than ff99 and also reproduces the curvature of the relative helix-Extended state energies. Therefore, the mathematical form of the Amber potential is sufficient to describe the local effect of 310-helix versus Extended Structure stabilization in the gas phase. However, the energy curves are shifted and the backbone geometries differ compared with the QM results. This may cause significant geometric discrepancies between native and predicted Structures. Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-Extended state energetics and geome- try of major conformations.
M L Goldstein - One of the best experts on this subject based on the ideXlab platform.
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wave vector dependence of magnetic turbulence spectra in the solar wind
Physical Review Letters, 2010Co-Authors: Yasuhito Narita, Karlheinz Glassmeier, F Sahraoui, M L GoldsteinAbstract:Using four-point measurements of the Cluster spacecraft, the energy distribution was determined for magnetic field fluctuations in the solar wind directly in the three-dimensional wave-vector domain in the range |k|{<=}1.5x10{sup -3} rad/km. The energy distribution exhibits anisotropic features characterized by a prominently Extended Structure perpendicular to the mean field preferring the ecliptic north direction and also by a moderately Extended Structure parallel to the mean field. From the three-dimensional energy distribution wave vector anisotropy is estimated with respect to directions parallel and perpendicular to the mean magnetic field, and the result suggests the dominance of quasi-two-dimensional turbulence toward smaller spatial scales.
Matthew J. Gage - One of the best experts on this subject based on the ideXlab platform.
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The insertion sequence of the N2A region of titin exists in an Extended Structure with helical characteristics Proteins and proteomics
Biochimica et Biophysica Acta, 2017Co-Authors: Holly Tiffany, Kanchan Sonkar, Matthew J. GageAbstract:The giant sarcomere protein titin is the third filament in muscle and is integral to maintaining sarcomere integrity as well as contributing to both active and passive tension. Titin is a multi-domain protein that contains regions of repeated structural elements. The N2A region sits at the boundary between the proximal Ig region of titin that is Extended under low force and the PEVK region that is Extended under high force. Multiple binding interactions have been associated with the N2A region and it has been proposed that this region acts as a mechanical stretch sensor. The focus of this work is a 117 amino acid portion of the N2A region (N2A-IS), which resides between the proximal Ig domains and the PEVK region. Our work has shown that the N2A-IS region is predicted to contain helical Structure in the center while both termini are predicted to be disordered. Recombinantly expressed N2A-IS protein contains 13% α-helical Structure, as measured via circular dichroism. Additional α-helical Structure can be induced with 2,2,2-trifluoroethanol, suggesting that there is transient helical Structure that might be stabilized in the context of the entire N2A region. The N2A-IS region does not exhibit any cooperativity in either thermal or chemical denaturation studies while size exclusion chromatography and Fluorescence Resonance Energy Transfer demonstrates that the N2A-IS region has an Extended Structure. Combined, these results lead to a model of the N2A-IS region having a helical core with Extended N- and C-termini.
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The insertion sequence of the N2A region of titin exists in an Extended Structure with helical characteristics.
Biochimica et biophysica acta. Proteins and proteomics, 2016Co-Authors: Holly Tiffany, Kanchan Sonkar, Matthew J. GageAbstract:The giant sarcomere protein titin is the third filament in muscle and is integral to maintaining sarcomere integrity as well as contributing to both active and passive tension. Titin is a multi-domain protein that contains regions of repeated structural elements. The N2A region sits at the boundary between the proximal Ig region of titin that is Extended under low force and the PEVK region that is Extended under high force. Multiple binding interactions have been associated with the N2A region and it has been proposed that this region acts as a mechanical stretch sensor. The focus of this work is a 117 amino acid portion of the N2A region (N2A-IS), which resides between the proximal Ig domains and the PEVK region. Our work has shown that the N2A-IS region is predicted to contain helical Structure in the center while both termini are predicted to be disordered. Recombinantly expressed N2A-IS protein contains 13% α-helical Structure, as measured via circular dichroism. Additional α-helical Structure can be induced with 2,2,2-trifluoroethanol, suggesting that there is transient helical Structure that might be stabilized in the context of the entire N2A region. The N2A-IS region does not exhibit any cooperativity in either thermal or chemical denaturation studies while size exclusion chromatography and Fluorescence Resonance Energy Transfer demonstrates that the N2A-IS region has an Extended Structure. Combined, these results lead to a model of the N2A-IS region having a helical core with Extended N- and C-termini.
W I Clarkson - One of the best experts on this subject based on the ideXlab platform.
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the quintuplet cluster Extended Structure and tidal radius
The Astrophysical Journal, 2019Co-Authors: Nicholas Z Rui, Matthew W Hosek, Jay Anderson, M Morris, W I Clarkson, A M GhezAbstract:Author(s): Rui, NZ; Hosek, MW; Lu, JR; Clarkson, WI; Anderson, J; Morris, MR; Ghez, AM | Abstract: © 2019. The American Astronomical Society. All rights reserved.. The Quintuplet star cluster is one of only three known young (l10 Myr) massive (M g 104 M o) clusters within ∼100 pc of the Galactic center (GC). In order to explore star cluster formation and evolution in this extreme environment, we analyze the Quintuplet's dynamical Structure. Using the HST WFC3-IR instrument, we take astrometric and photometric observations of the Quintuplet covering a 120″ × 120″ field of view, which is 19 times larger than those of previous proper-motion studies of the Quintuplet. We generate a catalog of the Quintuplet region with multiband, near-infrared photometry, proper motions, and cluster membership probabilities for 10,543 stars. We present the radial density profile of 715 candidate Quintuplet cluster members with M ≈ 4.7 M o out to 3.2 pc from the cluster center. A 3σ lower limit of 3 pc is placed on the tidal radius, indicating the lack of a tidal truncation within this radius range. Only weak evidence for mass segregation is found, in contrast to the strong mass segregation found in the Arches cluster, a second and slightly younger massive cluster near the GC. It is possible that tidal stripping hampers a mass segregation signature, though we find no evidence of spatial asymmetry. Assuming that the Arches and Quintuplet clusters formed with comparable extent, our measurement of the Quintuplet's comparatively large core radius of pc provides strong empirical evidence that young massive clusters in the GC dissolve on a several-megayear timescale.
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the quintuplet cluster Extended Structure and tidal radius
arXiv: Solar and Stellar Astrophysics, 2019Co-Authors: Nicholas Z Rui, Matthew W Hosek, Jay Anderson, M Morris, W I Clarkson, A M GhezAbstract:The Quintuplet star cluster is one of only three known young ($ 10^4$ M$_\odot$) clusters within $\sim100$ pc of the Galactic Center. In order to explore star cluster formation and evolution in this extreme environment, we analyze the Quintuplet's dynamical Structure. Using the HST WFC3-IR instrument, we take astrometric and photometric observations of the Quintuplet covering a $120''\times120''$ field-of-view, which is $19$ times larger than those of previous proper motion studies of the Quintuplet. We generate a catalog of the Quintuplet region with multi-band, near-infrared photometry, proper motions, and cluster membership probabilities for $10,543$ stars. We present the radial density profile of $715$ candidate Quintuplet cluster members with $M\gtrsim4.7$ M$_\odot$ out to $3.2$ pc from the cluster center. A $3\sigma$ lower limit of $3$ pc is placed on the tidal radius, indicating the lack of a tidal truncation within this radius range. Only weak evidence for mass segregation is found, in contrast to the strong mass segregation found in the Arches cluster, a second and slightly younger massive cluster near the Galactic Center. It is possible that tidal stripping hampers a mass segregation signature, though we find no evidence of spatial asymmetry. Assuming that the Arches and Quintuplet formed with comparable extent, our measurement of the Quintuplet's comparatively large core radius of $0.62^{+0.10}_{-0.10}$ pc provides strong empirical evidence that young massive clusters in the Galactic Center dissolve on a several Myr timescale.
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the arches cluster Extended Structure and tidal radius
The Astrophysical Journal, 2015Co-Authors: Matthew W Hosek, Jay Anderson, A M Ghez, M Morris, W I ClarksonAbstract:© 2015. The American Astronomical Society. All rights reserved. At a projected distance of ∼26 pc from Sgr A∗, the Arches cluster provides insight into star formation in the extreme Galactic center (GC) environment. Despite its importance, many key properties, such as the cluster's internal Structure and orbital history, are not well known. We present an astrometric and photometric study of the outer region of the Arches cluster (R > 6.″25) using Hubble Space Telescope WFC3IR. Using proper motions, we calculate membership probabilities for stars down to F153M = 20 mag (∼2.5 Mo) over a 120″ × 120″ field of view, an area 144 times larger than previous astrometric studies of the cluster. We construct the radial profile of the Arches to a radius of 75″ (∼3 pc at 8 kpc), which can be well described by a single power law. From this profile we place a 3σ lower limit of 2.8 pc on the observed tidal radius, which is larger than the predicted tidal radius (1-2.5 pc). Evidence of mass segregation is observed throughout the cluster, and no tidal tail Structures are apparent along the orbital path. The absence of breaks in the profile suggests that the Arches has not likely experienced its closest approach to the GC between ∼0.2 and 1 Myr ago. If accurate, this constraint indicates that the cluster is on a prograde orbit and is located in front of the sky plane that intersects Sgr A∗. However, further simulations of clusters in the GC potential are required to interpret the observed profile with more confidence.
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the arches cluster Extended Structure and tidal radius
arXiv: Solar and Stellar Astrophysics, 2015Co-Authors: Matthew W Hosek, Jay Anderson, A M Ghez, M Morris, W I ClarksonAbstract:At a projected distance of ~26 pc from Sgr A*, the Arches cluster provides insight to star formation in the extreme Galactic Center (GC) environment. Despite its importance, many key properties such as the cluster's internal Structure and orbital history are not well known. We present an astrometric and photometric study of the outer region of the Arches cluster (R > 6.25") using HST WFC3IR. Using proper motions we calculate membership probabilities for stars down to F153M = 20 mag (~2.5 M_sun) over a 120" x 120" field of view, an area 144 times larger than previous astrometric studies of the cluster. We construct the radial profile of the Arches to a radius of 75" (~3 pc at 8 kpc), which can be well described by a single power law. From this profile we place a 3-sigma lower limit of 2.8 pc on the observed tidal radius, which is larger than the predicted tidal radius (1 - 2.5 pc). Evidence of mass segregation is observed throughout the cluster and no tidal tail Structures are apparent along the orbital path. The absence of breaks in the profile suggests that the Arches has not likely experienced its closest approach to the GC between ~0.2 - 1 Myr ago. If accurate, this constraint indicates that the cluster is on a prograde orbit and is located front of the sky plane that intersects Sgr A*. However, further simulations of clusters in the GC potential are required to interpret the observed profile with more confidence.
A M Ghez - One of the best experts on this subject based on the ideXlab platform.
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the quintuplet cluster Extended Structure and tidal radius
The Astrophysical Journal, 2019Co-Authors: Nicholas Z Rui, Matthew W Hosek, Jay Anderson, M Morris, W I Clarkson, A M GhezAbstract:Author(s): Rui, NZ; Hosek, MW; Lu, JR; Clarkson, WI; Anderson, J; Morris, MR; Ghez, AM | Abstract: © 2019. The American Astronomical Society. All rights reserved.. The Quintuplet star cluster is one of only three known young (l10 Myr) massive (M g 104 M o) clusters within ∼100 pc of the Galactic center (GC). In order to explore star cluster formation and evolution in this extreme environment, we analyze the Quintuplet's dynamical Structure. Using the HST WFC3-IR instrument, we take astrometric and photometric observations of the Quintuplet covering a 120″ × 120″ field of view, which is 19 times larger than those of previous proper-motion studies of the Quintuplet. We generate a catalog of the Quintuplet region with multiband, near-infrared photometry, proper motions, and cluster membership probabilities for 10,543 stars. We present the radial density profile of 715 candidate Quintuplet cluster members with M ≈ 4.7 M o out to 3.2 pc from the cluster center. A 3σ lower limit of 3 pc is placed on the tidal radius, indicating the lack of a tidal truncation within this radius range. Only weak evidence for mass segregation is found, in contrast to the strong mass segregation found in the Arches cluster, a second and slightly younger massive cluster near the GC. It is possible that tidal stripping hampers a mass segregation signature, though we find no evidence of spatial asymmetry. Assuming that the Arches and Quintuplet clusters formed with comparable extent, our measurement of the Quintuplet's comparatively large core radius of pc provides strong empirical evidence that young massive clusters in the GC dissolve on a several-megayear timescale.
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the quintuplet cluster Extended Structure and tidal radius
arXiv: Solar and Stellar Astrophysics, 2019Co-Authors: Nicholas Z Rui, Matthew W Hosek, Jay Anderson, M Morris, W I Clarkson, A M GhezAbstract:The Quintuplet star cluster is one of only three known young ($ 10^4$ M$_\odot$) clusters within $\sim100$ pc of the Galactic Center. In order to explore star cluster formation and evolution in this extreme environment, we analyze the Quintuplet's dynamical Structure. Using the HST WFC3-IR instrument, we take astrometric and photometric observations of the Quintuplet covering a $120''\times120''$ field-of-view, which is $19$ times larger than those of previous proper motion studies of the Quintuplet. We generate a catalog of the Quintuplet region with multi-band, near-infrared photometry, proper motions, and cluster membership probabilities for $10,543$ stars. We present the radial density profile of $715$ candidate Quintuplet cluster members with $M\gtrsim4.7$ M$_\odot$ out to $3.2$ pc from the cluster center. A $3\sigma$ lower limit of $3$ pc is placed on the tidal radius, indicating the lack of a tidal truncation within this radius range. Only weak evidence for mass segregation is found, in contrast to the strong mass segregation found in the Arches cluster, a second and slightly younger massive cluster near the Galactic Center. It is possible that tidal stripping hampers a mass segregation signature, though we find no evidence of spatial asymmetry. Assuming that the Arches and Quintuplet formed with comparable extent, our measurement of the Quintuplet's comparatively large core radius of $0.62^{+0.10}_{-0.10}$ pc provides strong empirical evidence that young massive clusters in the Galactic Center dissolve on a several Myr timescale.
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the arches cluster Extended Structure and tidal radius
The Astrophysical Journal, 2015Co-Authors: Matthew W Hosek, Jay Anderson, A M Ghez, M Morris, W I ClarksonAbstract:© 2015. The American Astronomical Society. All rights reserved. At a projected distance of ∼26 pc from Sgr A∗, the Arches cluster provides insight into star formation in the extreme Galactic center (GC) environment. Despite its importance, many key properties, such as the cluster's internal Structure and orbital history, are not well known. We present an astrometric and photometric study of the outer region of the Arches cluster (R > 6.″25) using Hubble Space Telescope WFC3IR. Using proper motions, we calculate membership probabilities for stars down to F153M = 20 mag (∼2.5 Mo) over a 120″ × 120″ field of view, an area 144 times larger than previous astrometric studies of the cluster. We construct the radial profile of the Arches to a radius of 75″ (∼3 pc at 8 kpc), which can be well described by a single power law. From this profile we place a 3σ lower limit of 2.8 pc on the observed tidal radius, which is larger than the predicted tidal radius (1-2.5 pc). Evidence of mass segregation is observed throughout the cluster, and no tidal tail Structures are apparent along the orbital path. The absence of breaks in the profile suggests that the Arches has not likely experienced its closest approach to the GC between ∼0.2 and 1 Myr ago. If accurate, this constraint indicates that the cluster is on a prograde orbit and is located in front of the sky plane that intersects Sgr A∗. However, further simulations of clusters in the GC potential are required to interpret the observed profile with more confidence.
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the arches cluster Extended Structure and tidal radius
arXiv: Solar and Stellar Astrophysics, 2015Co-Authors: Matthew W Hosek, Jay Anderson, A M Ghez, M Morris, W I ClarksonAbstract:At a projected distance of ~26 pc from Sgr A*, the Arches cluster provides insight to star formation in the extreme Galactic Center (GC) environment. Despite its importance, many key properties such as the cluster's internal Structure and orbital history are not well known. We present an astrometric and photometric study of the outer region of the Arches cluster (R > 6.25") using HST WFC3IR. Using proper motions we calculate membership probabilities for stars down to F153M = 20 mag (~2.5 M_sun) over a 120" x 120" field of view, an area 144 times larger than previous astrometric studies of the cluster. We construct the radial profile of the Arches to a radius of 75" (~3 pc at 8 kpc), which can be well described by a single power law. From this profile we place a 3-sigma lower limit of 2.8 pc on the observed tidal radius, which is larger than the predicted tidal radius (1 - 2.5 pc). Evidence of mass segregation is observed throughout the cluster and no tidal tail Structures are apparent along the orbital path. The absence of breaks in the profile suggests that the Arches has not likely experienced its closest approach to the GC between ~0.2 - 1 Myr ago. If accurate, this constraint indicates that the cluster is on a prograde orbit and is located front of the sky plane that intersects Sgr A*. However, further simulations of clusters in the GC potential are required to interpret the observed profile with more confidence.
