{"id":"https://openalex.org/W110530439","doi":null,"title":"Probing the heme structure and environment of bacterial Heme-Nitric oxide/OXygen binding domains with resonance Raman spectroscopy","display_name":"Probing the heme structure and environment of bacterial Heme-Nitric oxide/OXygen binding domains with resonance Raman spectroscopy","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W110530439","mag":"110530439"},"language":"en","primary_location":{"id":"pmh:oai:escholarship.org/ark:/13030/qt6dh6g97q","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6dh6g97q","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},"volume":null,"type":"dissertation","indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111613865","display_name":"Rosalie Tran","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Rosalie Tran","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5111613865"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12094","display_name":"Hemoglobin structure and function","score":0.9193999767303467,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12094","display_name":"Hemoglobin structure and function","score":0.9193999767303467,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11747","display_name":"Metal-Catalyzed Oxygenation Mechanisms","score":0.06300000101327896,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11626","display_name":"Metalloenzymes and iron-sulfur proteins","score":0.0035000001080334187,"subfield":{"id":"https://openalex.org/subfields/2105","display_name":"Renewable Energy, Sustainability and the Environment"},"field":{"id":"https://openalex.org/fields/21","display_name":"Energy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/thermoanaerobacter-tengcongensis","display_name":"Thermoanaerobacter tengcongensis","score":0.8949999809265137},{"id":"https://openalex.org/keywords/heme-conformation","display_name":"heme conformation","score":0.722000002861023},{"id":"https://openalex.org/keywords/ligand-selectivity","display_name":"ligand selectivity","score":0.7099999785423279},{"id":"https://openalex.org/keywords/nitric-oxide-binding","display_name":"nitric oxide binding","score":0.8820000290870667},{"id":"https://openalex.org/keywords/oxygen-binding","display_name":"oxygen binding","score":0.9800000190734863},{"id":"https://openalex.org/keywords/c-o-stretching-frequency","display_name":"C=O stretching frequency","score":0.5809999704360962}],"concepts":[{"id":"https://openalex.org/C2776217839","wikidata":"https://www.wikidata.org/wiki/Q189621","display_name":"Heme","level":3,"score":0.8655816316604614},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7401167154312134},{"id":"https://openalex.org/C2781340169","wikidata":"https://www.wikidata.org/wiki/Q7315737","display_name":"Resonance Raman spectroscopy","level":3,"score":0.6770906448364258},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.55865079164505},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.5131021738052368},{"id":"https://openalex.org/C20705724","wikidata":"https://www.wikidata.org/wiki/Q902628","display_name":"Hemeprotein","level":4,"score":0.4994235038757324},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4886761009693146},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.48434460163116455},{"id":"https://openalex.org/C2778875234","wikidata":"https://www.wikidata.org/wiki/Q36626","display_name":"PAS domain","level":4,"score":0.47478243708610535},{"id":"https://openalex.org/C519581460","wikidata":"https://www.wikidata.org/wiki/Q207843","display_name":"Nitric oxide","level":2,"score":0.4210105538368225},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.3688047528266907},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.36523377895355225},{"id":"https://openalex.org/C40003534","wikidata":"https://www.wikidata.org/wiki/Q862228","display_name":"Raman spectroscopy","level":2,"score":0.21163597702980042},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.20336246490478516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16200771927833557},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.16076308488845825},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08418571949005127},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:escholarship.org/ark:/13030/qt6dh6g97q","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6dh6g97q","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"etd"},{"id":"pmh:qt6dh6g97q","doi":null,"is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/6dh6g97q","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Tran, Rosalie. (2010). Probing the heme structure and environment of bacterial Heme-Nitric oxide/OXygen binding domains with resonance Raman spectroscopy. UC Berkeley: Chemistry. Retrieved from: http://www.escholarship.org/uc/item/6dh6g97q","raw_type":"dissertation"},{"id":"mag:110530439","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6dh6g97q.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3048670414","https://openalex.org/W2059108388","https://openalex.org/W2479804505","https://openalex.org/W2007293244","https://openalex.org/W2329448053","https://openalex.org/W2904515213","https://openalex.org/W1980125903","https://openalex.org/W1974287747","https://openalex.org/W2002109628","https://openalex.org/W2168101142"],"abstract_inverted_index":{"The":[0,81,359],"Heme-Nitric":[1],"oxide/OXygen":[2],"binding":[3,57,440,517],"(H-NOX)":[4],"domain":[5,20],"encompasses":[6],"a":[7,125,173,213,520,575,585,610],"family":[8,130,285],"of":[9,21,48,84,131,141,161,172,180,278,283,290,327,349,366,397,420,436,450,462,469,490,588,612,625],"proteins":[10,183],"closely":[11],"related":[12],"(\u2264":[13],"40%":[14],"sequence":[15],"identity)":[16],"to":[17,62,94,114,149,232,235,310,388,399,411,452,482,493,502,571],"the":[18,26,46,69,97,116,135,151,162,170,195,203,208,227,247,256,270,287,298,312,315,321,338,342,347,350,355,367,370,374,391,406,412,418,421,425,429,434,437,444,453,459,467,470,483,488,494,498,503,510,515,526,531,543,557,589,599,602,606,622,633],"heme":[19,117,132,152,175,198,249,258,339,375,382,590,603,636],"soluble":[22],"guanylate":[23],"cyclase":[24],"(sGC),":[25],"eukaryotic":[27],"enzyme":[28],"receptor":[29],"for":[30,128,222,246,275,301],"NO":[31,37,43],"[1,":[32,78],"2].":[33],"sGC":[34],"discriminates":[35],"between":[36,334,369,528,601,635],"and":[38,40,75,111,138,144,191,206,237,320,337,373,390,464,530,563,605,615,629,638],"O2,":[39,67,532],"exclusively":[41],"binds":[42],"even":[44],"in":[45,106,119,202,226,307,442,458,473,545,593,641],"presence":[47,171],"excess":[49],"O2.":[50],"Although":[51],"some":[52],"H-NOX":[53,98,143,166,182,309,439,495,516,627],"domains":[54],"have":[55],"ligand":[56,86,157],"properties":[58,154,624],"that":[59,155,194,207,255,273,331,509,524],"are":[60],"identical":[61],"sGC,":[63],"others":[64],"additionally":[65],"bind":[66],"including":[68],"atypical":[70],"sGCs":[71],"from":[72,551,574],"Drosophila":[73],"melanogaster":[74],"Caenorhabditis":[76],"elegans":[77],"3,":[79],"4].":[80],"molecular":[82],"basis":[83],"this":[85,129,284,302,535,582,618,642],"selectivity":[87],"is":[88,169,286],"not":[89],"fully":[90],"understood.":[91],"In":[92,486],"order":[93],"better":[95],"understand":[96],"domain,":[99],"resonance":[100],"Raman":[101],"(RR)":[102],"spectroscopy":[103,614],"was":[104,260,385,447,456],"employed":[105],"combination":[107,611],"with":[108,266,553],"isotopic":[109],"substitution":[110],"site-directed":[112,616],"mutagenesis":[113],"probe":[115,311],"pocket":[118,272,441,496,518,608],"Thermoanaerobacter":[120],"tengcongensis":[121],"(Tt":[122],"H-NOX)":[123],"as":[124,240,242],"model":[126],"system":[127],"proteins.":[133],"Thus,":[134,538],"expression,":[136],"purification,":[137],"RR":[139,178,218,325,460,613],"characterization":[140],"Tt":[142,165,181,308,438,546,594],"selected":[145],"mutants":[146,329],"were":[147,220,305],"performed":[148],"elucidate":[150,297,621],"environmental":[153,591],"influence":[156,542],"binding.A":[158],"striking":[159],"feature":[160,282],"O2-bound":[163,204],"WT":[164,504],"crystal":[167],"structure":[168,637],"distorted":[174],"molecule":[176],"[5].":[177],"investigation":[179],"containing":[184],"mutations":[185,304,475],"at":[186],"key":[187],"conserved":[188,316,431],"residues,":[189],"Ile-5":[190],"Pro-115,":[192],"determined":[193],"most":[196,360,407],"dramatic":[197],"conformational":[199],"changes":[200,253],"occurred":[201,363],"forms,":[205],"single":[209],"P115A":[210,257],"mutation":[211],"generated":[212],"significantly":[214,340],"relaxed":[215,263],"chromophore.":[216],"Decreased":[217],"intensities":[219],"observed":[221],"several":[223],"out-of-plane":[224],"modes":[225],"400-750":[228],"cm-1":[229],"region":[230],"known":[231],"be":[233,417],"sensitive":[234],"ruffling":[236],"saddling":[238],"deformations,":[239],"well":[241],"increased":[243,267,476,525,556],"vibrational":[244],"frequencies":[245],"core":[248],"skeletal":[250],"modes.":[251],"These":[252,506],"demonstrated":[254,457],"conformation":[259],"considerably":[261],"more":[262,521,576],"than":[264],"WT,":[265,389],"flexibility":[268],"within":[269],"protein":[271,607,639],"allowed":[274],"rapid":[276],"sampling":[277],"alternate":[279],"conformations.Another":[280],"remarkable":[281],"spectroscopic":[288],"observation":[289],"an":[291],"unusually":[292],"high":[293],"\u03bd(C-O)":[294,395],"frequency.":[295],"To":[296],"interactions":[299,333,600],"responsible":[300],"property,":[303],"made":[306],"distal":[313,512],"pocket,":[314],"Tyr-Ser-Arg":[317],"(YxSxR)":[318],"motif,":[319],"heme-linkage":[322],"site":[323],"(His-102).":[324],"spectra":[326,461],"these":[328,335,404,474,626],"indicated":[330],"H-bonding":[332,552],"residues":[336,513],"affected":[341],"CO":[343,356],"bond":[344,572],"by":[345],"increasing":[346],"back-donation":[348],"FeII":[351],"d\u03c0":[352],"electrons":[353],"into":[354,519,632],"\u03c0*":[357],"orbitals.":[358],"significant":[361],"change":[362],"upon":[364,478,560],"disruption":[365,468],"H-bonds":[368,451],"YxSxR":[371,432],"motif":[372],"propionate":[376,426],"groups,":[377],"producing":[378],"two":[379,539],"dominant":[380],"CO-bound":[381],"conformations;":[383],"one":[384],"structurally":[386],"similar":[387],"other":[392],"conformer":[393],"displayed":[394],"downshifts":[396],"up":[398],"~70":[400],"cm-1.":[401],"Based":[402],"on":[403,424],"shifts,":[405],"important":[408],"factor":[409],"contributing":[410],"C-O":[413],"stretching":[414],"mode":[415],"may":[416,620],"neutralization":[419],"negative":[422],"charges":[423],"groups":[427],"via":[428],"strictly":[430],"motif.Finally,":[433],"role":[435],"stabilizing":[443],"O2":[445,455,579],"complex":[446],"investigated.":[448],"Evidence":[449],"bound":[454],"Trp-9":[463],"Tyr-140":[465,529],"mutants;":[466],"H-bond":[471],"network":[472],"\u03bd(Fe-O2)":[477,499,544,558,569],"returning":[479],"electron":[480],"density":[481],"Fe-O2":[484],"bond.":[485],"contrast,":[487],"addition":[489],"steric":[491,565],"bulk":[492],"decreased":[497,568],"frequency":[500,559],"relative":[501],"protein.":[505],"shifts":[507],"suggested":[508],"bulky":[511],"forced":[514],"open":[522],"position":[523],"distance":[527],"thereby":[533],"weakening":[534],"crucial":[536],"H-bond.":[537],"distinct":[540],"factors":[541],"H-NOX:":[547],"(i)":[548],"electrostatic":[549],"effects":[550,566,592],"Tyr-140,":[554],"which":[555,567],"its":[561],"removal;":[562],"(ii)":[564],"due":[570],"lengthening":[573],"loosely":[577],"held":[578],"ligand.In":[580],"summary,":[581],"work":[583],"presents":[584],"comparative":[586],"analysis":[587],"H-NOX.":[595],"By":[596],"directly":[597],"probing":[598],"chromophore":[604],"through":[609],"mutagenesis,":[617],"study":[619],"biochemical":[623],"domains,":[628],"bring":[630],"insight":[631],"relationship":[634],"function":[640],"family.":[643]},"counts_by_year":[],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2016-06-24T00:00:00"}
