Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N‑Termini
R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids...
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Veröffentlicht in: | Biochemistry (Easton) 2017-11, Vol.56 (44), p.5886-5899 |
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creator | Bhojane, Purva P Duff, Michael R Bafna, Khushboo Agarwal, Pratul Stanley, Christopher Howell, Elizabeth E |
description | R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (R g) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the R g increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated. |
doi_str_mv | 10.1021/acs.biochem.7b00822 |
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(ORNL), Oak Ridge, TN (United States)</creatorcontrib><description>R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (R g) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the R g increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated.</description><identifier>ISSN: 0006-2960</identifier><identifier>ISSN: 1520-4995</identifier><identifier>EISSN: 1520-4995</identifier><identifier>DOI: 10.1021/acs.biochem.7b00822</identifier><identifier>PMID: 29020453</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>60 APPLIED LIFE SCIENCES ; active sites ; amino acids ; apoproteins ; betaine ; Betaine - pharmacology ; calorimetry ; chymotrypsin ; Chymotrypsin - metabolism ; crystal structure ; dihydrofolate reductase ; dimethyl sulfoxide ; Escherichia coli ; Escherichia coli Proteins - chemistry ; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY ; molecular dynamics ; Molecular Dynamics Simulation ; Neutron Diffraction ; neutrons ; Protein Conformation ; Protein Structure, Secondary ; Scattering, Small Angle ; setae (animal) ; Tetrahydrofolate Dehydrogenase - chemistry ; trimethoprim ; Water - metabolism</subject><ispartof>Biochemistry (Easton), 2017-11, Vol.56 (44), p.5886-5899</ispartof><rights>Copyright © 2017 American Chemical Society 2017 American Chemical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a505t-905de0fb4eb2cdd2b9d5e923d0b70903db785001b94e3210d89b7b2d91d572623</citedby><cites>FETCH-LOGICAL-a505t-905de0fb4eb2cdd2b9d5e923d0b70903db785001b94e3210d89b7b2d91d572623</cites><orcidid>0000-0001-6157-433X ; 0000-0002-3848-9492 ; 0000-0002-4226-7710 ; 0000000238489492 ; 0000000242267710 ; 000000016157433X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.biochem.7b00822$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.biochem.7b00822$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>230,314,778,782,883,2754,27059,27907,27908,56721,56771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29020453$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1407720$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Bhojane, Purva P</creatorcontrib><creatorcontrib>Duff, Michael R</creatorcontrib><creatorcontrib>Bafna, Khushboo</creatorcontrib><creatorcontrib>Agarwal, Pratul</creatorcontrib><creatorcontrib>Stanley, Christopher</creatorcontrib><creatorcontrib>Howell, Elizabeth E</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N‑Termini</title><title>Biochemistry (Easton)</title><addtitle>Biochemistry</addtitle><description>R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (R g) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the R g increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>active sites</subject><subject>amino acids</subject><subject>apoproteins</subject><subject>betaine</subject><subject>Betaine - pharmacology</subject><subject>calorimetry</subject><subject>chymotrypsin</subject><subject>Chymotrypsin - metabolism</subject><subject>crystal structure</subject><subject>dihydrofolate reductase</subject><subject>dimethyl sulfoxide</subject><subject>Escherichia coli</subject><subject>Escherichia coli Proteins - chemistry</subject><subject>INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY</subject><subject>molecular dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Neutron Diffraction</subject><subject>neutrons</subject><subject>Protein Conformation</subject><subject>Protein Structure, Secondary</subject><subject>Scattering, Small Angle</subject><subject>setae (animal)</subject><subject>Tetrahydrofolate Dehydrogenase - chemistry</subject><subject>trimethoprim</subject><subject>Water - metabolism</subject><issn>0006-2960</issn><issn>1520-4995</issn><issn>1520-4995</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks1u1DAUhSMEokPhCZCQxYoFmd44cRJvkKpSoFJVUGdYW_65M-MqsYvtUM2ODQ_AK_IkeDRDBRvY2LLuOd-9tk9RPK9gXgGtTqSOc2W93uA47xRAT-mDYlYxCmXDOXtYzACgLSlv4ah4EuNNPjbQNY-LI8qBQsPqWfF9McphIKduPSC5wikF78hCy5QwWLcmizQZi5H4FbluO_LWbrYm-JUfZEJyjWbSSUZ8TSRZYgpyzC5NPgWf0DpyZ9OGXLiUSdHq3GebAdEHgwENufr57ccSw2idfVo8Wskh4rPDflx8fne-PPtQXn58f3F2ellKBiyVHJhBWKkGFdXGUMUNQ05rA6oDDrVRXc8AKsUbrGkFpueqU9TwyrCOtrQ-Lt7subeTGtFozLPJQdwGO8qwFV5a8XfF2Y1Y-6-CtV3f8yYDXu4BPiYrorYJ9UZ751AnUeXX7Shk0atDl-C_TBiTGG3UOAzSoZ-ioMDqvq056_4rrTiDJi_1bvZ6L9XBxxhwdT92BWIXCJEDIQ6BEIdAZNeLP2987_mdgCw42Qt27hs_BZc_4J_IX_pexvo</recordid><startdate>20171107</startdate><enddate>20171107</enddate><creator>Bhojane, Purva P</creator><creator>Duff, Michael R</creator><creator>Bafna, Khushboo</creator><creator>Agarwal, Pratul</creator><creator>Stanley, Christopher</creator><creator>Howell, Elizabeth E</creator><general>American Chemical Society</general><general>American Chemical Society (ACS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>OTOTI</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-6157-433X</orcidid><orcidid>https://orcid.org/0000-0002-3848-9492</orcidid><orcidid>https://orcid.org/0000-0002-4226-7710</orcidid><orcidid>https://orcid.org/0000000238489492</orcidid><orcidid>https://orcid.org/0000000242267710</orcidid><orcidid>https://orcid.org/000000016157433X</orcidid></search><sort><creationdate>20171107</creationdate><title>Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N‑Termini</title><author>Bhojane, Purva P ; Duff, Michael R ; Bafna, Khushboo ; Agarwal, Pratul ; Stanley, Christopher ; Howell, Elizabeth E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a505t-905de0fb4eb2cdd2b9d5e923d0b70903db785001b94e3210d89b7b2d91d572623</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>60 APPLIED LIFE SCIENCES</topic><topic>active sites</topic><topic>amino acids</topic><topic>apoproteins</topic><topic>betaine</topic><topic>Betaine - pharmacology</topic><topic>calorimetry</topic><topic>chymotrypsin</topic><topic>Chymotrypsin - metabolism</topic><topic>crystal structure</topic><topic>dihydrofolate reductase</topic><topic>dimethyl sulfoxide</topic><topic>Escherichia coli</topic><topic>Escherichia coli Proteins - chemistry</topic><topic>INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY</topic><topic>molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Neutron Diffraction</topic><topic>neutrons</topic><topic>Protein Conformation</topic><topic>Protein Structure, Secondary</topic><topic>Scattering, Small Angle</topic><topic>setae (animal)</topic><topic>Tetrahydrofolate Dehydrogenase - chemistry</topic><topic>trimethoprim</topic><topic>Water - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bhojane, Purva P</creatorcontrib><creatorcontrib>Duff, Michael R</creatorcontrib><creatorcontrib>Bafna, Khushboo</creatorcontrib><creatorcontrib>Agarwal, Pratul</creatorcontrib><creatorcontrib>Stanley, Christopher</creatorcontrib><creatorcontrib>Howell, Elizabeth E</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biochemistry (Easton)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bhojane, Purva P</au><au>Duff, Michael R</au><au>Bafna, Khushboo</au><au>Agarwal, Pratul</au><au>Stanley, Christopher</au><au>Howell, Elizabeth E</au><aucorp>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N‑Termini</atitle><jtitle>Biochemistry (Easton)</jtitle><addtitle>Biochemistry</addtitle><date>2017-11-07</date><risdate>2017</risdate><volume>56</volume><issue>44</issue><spage>5886</spage><epage>5899</epage><pages>5886-5899</pages><issn>0006-2960</issn><issn>1520-4995</issn><eissn>1520-4995</eissn><abstract>R67 dihydrofolate reductase (DHFR) is a homotetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site-directed inhibitor of Escherichia coli DHFR. Sixteen to twenty N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with a decreased stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering. From a combined analysis using molecular dynamics and the program SASSIE (http://www.smallangles.net/sassie/SASSIE_HOME.html), the apoenzyme displays a radius of gyration (R g) of 21.46 ± 0.50 Å. Addition of glycine betaine, an osmolyte, does not result in folding of the termini as the R g increases slightly to 22.78 ± 0.87 Å. SASSIE fits of the latter SANS data indicate that the disordered N-termini sample larger regions of space and remain disordered, suggesting they might function as entropic bristles. Pressure perturbation calorimetry also indicated that the volume of R67 DHFR increases upon addition of 10% betaine and decreased at 20% betaine because of the dehydration of the protein. Studies of the hydration of full-length R67 DHFR in the presence of the osmolytes betaine and dimethyl sulfoxide find around 1250 water molecules hydrating the protein. Similar studies with truncated R67 DHFR yield around 400 water molecules hydrating the protein in the presence of betaine. The difference of ∼900 waters indicates the N-termini are well-hydrated.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>29020453</pmid><doi>10.1021/acs.biochem.7b00822</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0001-6157-433X</orcidid><orcidid>https://orcid.org/0000-0002-3848-9492</orcidid><orcidid>https://orcid.org/0000-0002-4226-7710</orcidid><orcidid>https://orcid.org/0000000238489492</orcidid><orcidid>https://orcid.org/0000000242267710</orcidid><orcidid>https://orcid.org/000000016157433X</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | 60 APPLIED LIFE SCIENCES active sites amino acids apoproteins betaine Betaine - pharmacology calorimetry chymotrypsin Chymotrypsin - metabolism crystal structure dihydrofolate reductase dimethyl sulfoxide Escherichia coli Escherichia coli Proteins - chemistry INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY molecular dynamics Molecular Dynamics Simulation Neutron Diffraction neutrons Protein Conformation Protein Structure, Secondary Scattering, Small Angle setae (animal) Tetrahydrofolate Dehydrogenase - chemistry trimethoprim Water - metabolism |
title | Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N‑Termini |
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