The Experts below are selected from a list of 75 Experts worldwide ranked by ideXlab platform
Haruki Nakamura - One of the best experts on this subject based on the ideXlab platform.
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energy landsCape of a peptide Consisting of α helix 310 helix β turn β hairpin and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
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Energy landsCape of a peptide Consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
Junichi Higo - One of the best experts on this subject based on the ideXlab platform.
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energy landsCape of a peptide Consisting of α helix 310 helix β turn β hairpin and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
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Energy landsCape of a peptide Consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
Masataka Kuroda - One of the best experts on this subject based on the ideXlab platform.
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energy landsCape of a peptide Consisting of α helix 310 helix β turn β hairpin and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
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Energy landsCape of a peptide Consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
Nobuyuki Nakajima - One of the best experts on this subject based on the ideXlab platform.
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energy landsCape of a peptide Consisting of α helix 310 helix β turn β hairpin and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
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Energy landsCape of a peptide Consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered Conformations
Protein Science, 2001Co-Authors: Junichi Higo, Masataka Kuroda, Nobuyuki Nakajima, Haruki NakamuraAbstract:The energy landsCape of a peptide [ACe-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in expliCit water was studied with a multiCanoniCal moleCular dynamiCs simulation, and the AMBER parm96 forCe field was used for the energy CalCulation. The peptide was taken from the reCognition helix of the DNA-binding Protein, C-Myb. A rugged energy landsCape was obtained, in whiCh the random-Coil Conformations were dominant at room temperature. The CD speCtra of the synthesized peptide revealed that it is in the random state at room temperature. However, the 300 K CanoniCal ensemble, Q(300K), Contained α-helix, 310-helix, β-turn, and β-hairpin struCtures with small but notable probabilities of existenCe. The Complete α-helix, imperfeCt α-helix, and random-Coil Conformations were separated from one another in the Conformational spaCe. This means that the peptide must overCome energy barriers to form the α-helix. The overComing proCess may Correspond to the hydrogen-bond rearrangements from peptide–water to peptide–peptide interaCtions. The β-turn, imperfeCt 310-helix, and β-hairpin struCtures, among whiCh there are no energy barriers at 300 K, were embedded in the ensemble of the random-Coil Conformations. Two types of β-hairpin with different β-turn regions were observed in Q(300K). The two β-hairpin struCtures may have different meChanisms for the β-hairpin formation. The Current study proposes a sCheme that the random state of this peptide Consists of both ordered and disordered Conformations. In Contrast, the energy landsCape obtained from the parm94 forCe field was funnel like, in whiCh the peptide formed the heliCal Conformation at room temperature and random Coil at high temperature.
Turkan Haliloglu - One of the best experts on this subject based on the ideXlab platform.
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Conformational Control of the binding of the transaCtivation domain of the mll Protein and C Myb to the kix domain of Creb
PLOS Computational Biology, 2012Co-Authors: Elif Nihal Korkmaz, Ruth Nussinov, Turkan HalilogluAbstract:The KIX domain of CBP is a transCriptional CoaCtivator. ConComitant binding to the aCtivation domain of proto-onCogene Protein C-Myb and the transaCtivation domain of the trithorax group Protein mixed lineage leukemia (MLL) transCription faCtor lead to the biologiCally aCtive ternary MLL:KIX:C-Myb Complex whiCh plays a role in Pol II-mediated transCription. The binding of the aCtivation domain of MLL to KIX enhanCes C-Myb binding. Here we Carried out moleCular dynamiCs (MD) simulations for the MLL:KIX:C-Myb ternary Complex, its binary Components and KIX with the goal of providing a meChanistiC explanation for the experimental observations. The dynamiC behavior revealed that the MLL binding site is allosteriCally Coupled to the C-Myb binding site. MLL binding redistributes the Conformational ensemble of KIX, leading to higher populations of states whiCh favor C-Myb binding. The key element in the allosteriC CommuniCation pathways is the KIX loop, whiCh aCts as a Control meChanism to enhanCe subsequent binding events. We tested this ConClusion by in siliCo mutations of loop residues in the KIX:MLL Complex and by Comparing wild type and mutant dynamiCs through MD simulations. The loop assumed MLL binding Conformation similar to that observed in the KIX:C-Myb state whiCh disfavors the allosteriC network. The Coupling with C-Myb binding site faded, abolishing the positive Cooperativity observed in the presenCe of MLL. Our major ConClusion is that by eliCiting a loop-mediated allosteriC switCh between the different states following the binding events, transCriptional aCtivation Can be regulated. The KIX system presents an example how nature makes use of Conformational Control in higher level regulation of transCriptional aCtivity and thus Cellular events.
