{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2010:PWHQ7X6WW5DBSETYY7QG7OZ3AK","short_pith_number":"pith:PWHQ7X6W","schema_version":"1.0","canonical_sha256":"7d8f0fdfd6b746191278c7e06fbb3b029a28e11da1d69bc879fc3329fa567850","source":{"kind":"arxiv","id":"1012.4628","version":1},"attestation_state":"computed","paper":{"title":"Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.bio-ph","physics.chem-ph","q-bio.BM"],"primary_cat":"cond-mat.stat-mech","authors_text":"Bharat V. Adkar, Biman Bagchi, Biman Jana","submitted_at":"2010-12-21T12:24:00Z","abstract_excerpt":"The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the release of two ADP molecules. We have computed a novel two dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, with explicit interactions with water. Our computed 2DCFES clearly reveals the existence of a stable half-open-half-closed (HOHC) intermediate state of the enzyme. Cycli"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1012.4628","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cond-mat.stat-mech","submitted_at":"2010-12-21T12:24:00Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph","q-bio.BM"],"title_canon_sha256":"949b24a988ece48889a22adc8943ead073a8f70b06c5560d786b3a0fe6fab2c9","abstract_canon_sha256":"258e04816f4abe0ba2402000e47b9061b6bf9cbee0c3c38539959d47fa56eacf"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T04:32:54.003355Z","signature_b64":"951ZN471MemGs/EQRsMJYaMypNzA5POQda3OdptdXQjy9vfGotcSmZCy2JHWeU+0GYgMCeRbuLSjy8VTuxUJAg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"7d8f0fdfd6b746191278c7e06fbb3b029a28e11da1d69bc879fc3329fa567850","last_reissued_at":"2026-05-18T04:32:54.002956Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T04:32:54.002956Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.bio-ph","physics.chem-ph","q-bio.BM"],"primary_cat":"cond-mat.stat-mech","authors_text":"Bharat V. Adkar, Biman Bagchi, Biman Jana","submitted_at":"2010-12-21T12:24:00Z","abstract_excerpt":"The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the release of two ADP molecules. We have computed a novel two dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, with explicit interactions with water. Our computed 2DCFES clearly reveals the existence of a stable half-open-half-closed (HOHC) intermediate state of the enzyme. Cycli"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1012.4628","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"1012.4628","created_at":"2026-05-18T04:32:54.003018+00:00"},{"alias_kind":"arxiv_version","alias_value":"1012.4628v1","created_at":"2026-05-18T04:32:54.003018+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1012.4628","created_at":"2026-05-18T04:32:54.003018+00:00"},{"alias_kind":"pith_short_12","alias_value":"PWHQ7X6WW5DB","created_at":"2026-05-18T12:26:12.377268+00:00"},{"alias_kind":"pith_short_16","alias_value":"PWHQ7X6WW5DBSETY","created_at":"2026-05-18T12:26:12.377268+00:00"},{"alias_kind":"pith_short_8","alias_value":"PWHQ7X6W","created_at":"2026-05-18T12:26:12.377268+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK","json":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK.json","graph_json":"https://pith.science/api/pith-number/PWHQ7X6WW5DBSETYY7QG7OZ3AK/graph.json","events_json":"https://pith.science/api/pith-number/PWHQ7X6WW5DBSETYY7QG7OZ3AK/events.json","paper":"https://pith.science/paper/PWHQ7X6W"},"agent_actions":{"view_html":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK","download_json":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK.json","view_paper":"https://pith.science/paper/PWHQ7X6W","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1012.4628&json=true","fetch_graph":"https://pith.science/api/pith-number/PWHQ7X6WW5DBSETYY7QG7OZ3AK/graph.json","fetch_events":"https://pith.science/api/pith-number/PWHQ7X6WW5DBSETYY7QG7OZ3AK/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK/action/timestamp_anchor","attest_storage":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK/action/storage_attestation","attest_author":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK/action/author_attestation","sign_citation":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK/action/citation_signature","submit_replication":"https://pith.science/pith/PWHQ7X6WW5DBSETYY7QG7OZ3AK/action/replication_record"}},"created_at":"2026-05-18T04:32:54.003018+00:00","updated_at":"2026-05-18T04:32:54.003018+00:00"}