The human voltage-gated proton channels (hHV1) are critical in many physiological functions and control proton conduction in the cell. This process is governed by the cooperative response of different transmembrane segments of the protein. It is believed that the two subunits of the C-terminal dimer provide independent proton channel pathways through the membrane where the conformations of both monomers and dimer are key for selective proton transport. Conformational response of these transmembrane segments of the protein hHV1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored and its specificity is captured by its unique interaction. How residues of the protein hHv1 assemble or disperse as the temperature varies is addressed using a coarse-grained Monte Carlo simulation where a knowledge-based residue-residue interaction matrix is used as input in the Metropolis algorithm. Contact maps, mobility, radius of gyration, and structure factors, are examined as functions of temperature due to the efficiency of this model. Thermal response of the radius of gyration of this protein in the low-temperature regime decreases on increasing temperature in which structure becomes more compact by reduced entropy while in the high-temperature regime, the radius of gyration increases with temperature before reaching a steady state value. The scaling of structure factor S(q) provides an estimate of the effective dimension (D) of the protein chain which becomes globular conformation (D~3) with more connectedness in the low-temperature region and random coil (D~2) and then linear conformation (D~1) on increasing temperature further.
","abstract_html":"<p>The human voltage-gated proton channels (hH<sub>V</sub>1) are critical in many physiological functions and control proton conduction in the cell. This process is governed by the cooperative response of different transmembrane segments of the protein. It is believed that the two subunits of the C-terminal dimer provide independent proton channel pathways through the membrane where the conformations of both monomers and dimer are key for selective proton transport. Conformational response of these transmembrane segments of the protein hH<sub>V</sub>1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored and its specificity is captured by its unique interaction. How residues of the protein hH<sub>v</sub>1 assemble or disperse as the temperature varies is addressed using a coarse-grained Monte Carlo simulation where a knowledge-based residue-residue interaction matrix is used as input in the Metropolis algorithm. Contact maps, mobility, radius of gyration, and structure factors, are examined as functions of temperature due to the efficiency of this model. Thermal response of the radius of gyration of this protein in the low-temperature regime decreases on increasing temperature in which structure becomes more compact by reduced entropy while in the high-temperature regime, the radius of gyration increases with temperature before reaching a steady state value. The scaling of structure factor <em>S(q)</em> provides an estimate of the effective dimension (D) of the protein chain which becomes globular conformation (D~3) with more connectedness in the low-temperature region and random coil (D~2) and then linear conformation (D~1) on increasing temperature further.</p>","abstract_has_math":false,"creators":["Paudel, Sunita Subedi"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Masters Thesis","degree_discipline":"Physics and Astronomy","degree_department":null,"school":null,"contributors":["Ras B. Pandey","Christopher Winstead","Michael D. Vera"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017-08-01T07:00:00Z","date_published":"2017-08-01T07:00:00Z","updated_at":"2026-07-24T05:44:50Z","subjects":["Protein Folding","Statistical Analysis of Membrane protein","Channel protein","Voltage-gated proton channel"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://aquila.usm.edu/masters_theses/312","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Ras B. Pandey","Christopher Winstead","Michael D. Vera"]},{"key":"dc:creator","label":"Author","values":["Paudel, Sunita Subedi"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2017-06-29T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Physics and Astronomy"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Masters Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Protein Folding","Statistical Analysis of Membrane protein","Channel protein","Voltage-gated proton channel"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://aquila.usm.edu/masters_theses/312"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The human voltage-gated proton channels (hHV1) are critical in many physiological functions and control proton conduction in the cell. This process is governed by the cooperative response of different transmembrane segments of the protein. It is believed that the two subunits of the C-terminal dimer provide independent proton channel pathways through the membrane where the conformations of both monomers and dimer are key for selective proton transport. Conformational response of these transmembrane segments of the protein hHV1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored and its specificity is captured by its unique interaction. How residues of the protein hHv1 assemble or disperse as the temperature varies is addressed using a coarse-grained Monte Carlo simulation where a knowledge-based residue-residue interaction matrix is used as input in the Metropolis algorithm. Contact maps, mobility, radius of gyration, and structure factors, are examined as functions of temperature due to the efficiency of this model. Thermal response of the radius of gyration of this protein in the low-temperature regime decreases on increasing temperature in which structure becomes more compact by reduced entropy while in the high-temperature regime, the radius of gyration increases with temperature before reaching a steady state value. The scaling of structure factor S(q) provides an estimate of the effective dimension (D) of the protein chain which becomes globular conformation (D~3) with more connectedness in the low-temperature region and random coil (D~2) and then linear conformation (D~1) on increasing temperature further.
"]},{"key":"dc:title","label":"Title","values":["Conformation of Transmembrane Segments of a Protein by a Coarse Grain Model"]}]}],"canonical_facts":{"dc:contributor":["Ras B. Pandey","Christopher Winstead","Michael D. Vera"],"dc:creator":["Paudel, Sunita Subedi"],"dc:date.available":["2017-06-29T07:00:00Z"],"dc:description.abstract":["The human voltage-gated proton channels (hHV1) are critical in many physiological functions and control proton conduction in the cell. This process is governed by the cooperative response of different transmembrane segments of the protein. It is believed that the two subunits of the C-terminal dimer provide independent proton channel pathways through the membrane where the conformations of both monomers and dimer are key for selective proton transport. Conformational response of these transmembrane segments of the protein hHV1 is studied by a coarse-grained model as a function of temperature where structural detail of a residue is ignored and its specificity is captured by its unique interaction. How residues of the protein hHv1 assemble or disperse as the temperature varies is addressed using a coarse-grained Monte Carlo simulation where a knowledge-based residue-residue interaction matrix is used as input in the Metropolis algorithm. Contact maps, mobility, radius of gyration, and structure factors, are examined as functions of temperature due to the efficiency of this model. Thermal response of the radius of gyration of this protein in the low-temperature regime decreases on increasing temperature in which structure becomes more compact by reduced entropy while in the high-temperature regime, the radius of gyration increases with temperature before reaching a steady state value. The scaling of structure factor S(q) provides an estimate of the effective dimension (D) of the protein chain which becomes globular conformation (D~3) with more connectedness in the low-temperature region and random coil (D~2) and then linear conformation (D~1) on increasing temperature further.
"],"dc:identifier":["https://aquila.usm.edu/masters_theses/312"],"dc:subject":["Protein Folding","Statistical Analysis of Membrane protein","Channel protein","Voltage-gated proton channel"],"dc:title":["Conformation of Transmembrane Segments of a Protein by a Coarse Grain Model"],"thesis:degree_discipline":["Physics and Astronomy"],"thesis:degree_level":["Masters Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T05:44:50Z"}