{"id":{"repo_id":"njit","oai_identifier":"oai:digitalcommons.njit.edu:theses-1483"},"canonical_url":"https://search.dev.ndltd.org/etd/njit/oai:digitalcommons.njit.edu:theses-1483","repository":{"repo_id":"njit","name":"NJIT","base_url":"https://digitalcommons.njit.edu/do/oai/"},"display":{"title":"Structure and dynamics of soluble guanylyl cyclase","abstract":"Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation. From these MD simulations, a tentative mechanism of sGC activation is established. The difference in the initial binding modes of YC-l in its binding pocket results in different conformational changes in the active site of sGC, which results in different catalytic capability. Meanwhile, YC-l was found to be strongly attracted to [alpha]_1 CYS594, a residue deep inside of the allosteric binding pocket.","abstract_html":"Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation. From these MD simulations, a tentative mechanism of sGC activation is established. The difference in the initial binding modes of YC-l in its binding pocket results in different conformational changes in the active site of sGC, which results in different catalytic capability. Meanwhile, YC-l was found to be strongly attracted to [alpha]_1 CYS594, a residue deep inside of the allosteric binding pocket.","abstract_has_math":false,"creators":["Sugino, Kentaro"],"institution":null,"degree_name":"Master of Science in Computational Biology - (M.S.)","degree_level":null,"degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Qun Ma","Frank Y. Shih","Alexandros V. Gerbessiotis"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2005,"date_issued":"2005-05-31T07:00:00Z","date_published":"2005-05-31T07:00:00Z","updated_at":"2026-07-24T03:23:27Z","subjects":["Soluble guanylyl cyclase","3D structure","Biostatistics","Computer Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.njit.edu/theses/484","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Qun Ma","Frank Y. Shih","Alexandros V. Gerbessiotis"]},{"key":"dc:creator","label":"Author","values":["Sugino, Kentaro"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science in Computational Biology - (M.S.)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Soluble guanylyl cyclase","3D structure","Biostatistics","Computer Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.njit.edu/theses/484"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation. From these MD simulations, a tentative mechanism of sGC activation is established. The difference in the initial binding modes of YC-l in its binding pocket results in different conformational changes in the active site of sGC, which results in different catalytic capability. Meanwhile, YC-l was found to be strongly attracted to [alpha]_1 CYS594, a residue deep inside of the allosteric binding pocket."]},{"key":"dc:title","label":"Title","values":["Structure and dynamics of soluble guanylyl cyclase"]}]}],"canonical_facts":{"dc:contributor":["Qun Ma","Frank Y. Shih","Alexandros V. Gerbessiotis"],"dc:creator":["Sugino, Kentaro"],"dc:description.abstract":["Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation. From these MD simulations, a tentative mechanism of sGC activation is established. The difference in the initial binding modes of YC-l in its binding pocket results in different conformational changes in the active site of sGC, which results in different catalytic capability. Meanwhile, YC-l was found to be strongly attracted to [alpha]_1 CYS594, a residue deep inside of the allosteric binding pocket."],"dc:identifier":["https://digitalcommons.njit.edu/theses/484"],"dc:subject":["Soluble guanylyl cyclase","3D structure","Biostatistics","Computer Sciences"],"dc:title":["Structure and dynamics of soluble guanylyl cyclase"],"dc:type":["Thesis"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_name":["Master of Science in Computational Biology - (M.S.)"]},"updated_at":"2026-07-24T03:23:27Z"}