Using isoelectric point to determine the pH for initial protein crystallization trials
The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, t...
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| Veröffentlicht in: | Bioinformatics 2015-05, Vol.31 (9), p.1444-1451 |
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| creator | Kirkwood, Jobie Hargreaves, David O'Keefe, Simon Wilson, Julie |
| description | The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.
Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.
Data used to generate models are available as Supplementary Material.
julie.wilson@york.ac.uk
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btv011 |
| format | Article |
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Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.
Data used to generate models are available as Supplementary Material.
julie.wilson@york.ac.uk
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>EISSN: 1460-2059</identifier><identifier>DOI: 10.1093/bioinformatics/btv011</identifier><identifier>PMID: 25573921</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Bioinformatics ; Buffer solutions ; Buffers ; Crystallization ; Estimates ; Hydrogen-Ion Concentration ; Isoelectric Point ; Mathematical models ; Original Papers ; Proteins ; Proteins - chemistry</subject><ispartof>Bioinformatics, 2015-05, Vol.31 (9), p.1444-1451</ispartof><rights>The Author 2015. Published by Oxford University Press.</rights><rights>The Author 2015. Published by Oxford University Press. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c543t-ae32797892e40f67961f5b0e6cbb09e5160486d315502bd7455128c2daa54f9f3</citedby><cites>FETCH-LOGICAL-c543t-ae32797892e40f67961f5b0e6cbb09e5160486d315502bd7455128c2daa54f9f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410668/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410668/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25573921$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kirkwood, Jobie</creatorcontrib><creatorcontrib>Hargreaves, David</creatorcontrib><creatorcontrib>O'Keefe, Simon</creatorcontrib><creatorcontrib>Wilson, Julie</creatorcontrib><title>Using isoelectric point to determine the pH for initial protein crystallization trials</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.
Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.
Data used to generate models are available as Supplementary Material.
julie.wilson@york.ac.uk
Supplementary data are available at Bioinformatics online.</description><subject>Bioinformatics</subject><subject>Buffer solutions</subject><subject>Buffers</subject><subject>Crystallization</subject><subject>Estimates</subject><subject>Hydrogen-Ion Concentration</subject><subject>Isoelectric Point</subject><subject>Mathematical models</subject><subject>Original Papers</subject><subject>Proteins</subject><subject>Proteins - chemistry</subject><issn>1367-4803</issn><issn>1367-4811</issn><issn>1460-2059</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkV9rFTEQxUNR2nrbj6Dk0ZdrJ5t_mxdBSrVCwRfra8hmZ9vIbrImuYX66Y3cerFvfZqBOfObMxxC3jL4wMDwiyGkEKeUF1eDLxdDfQDGjsgp40pvRc_Yq0MP_IS8KeUnAEiQ6picdFJqbjp2Sn7clhDvaCgJZ_Q1B0_XBq60JjpixbyEiLTeI12vaTtHQww1uJmuOVUMkfr8WKqb5_C7GUmRNoSbyxl5PbWC5091Q24_X32_vN7efPvy9fLTzdZLwevWIe-00b3pUMCktFFskgOg8sMABiVTIHo1ciYldMOohZSs6303OifFZCa-IR_33HU3LDh6jDW72a45LC4_2uSCfT6J4d7epQcrBAOl-gZ4_wTI6dcOS7VLKB7n2UVMu2KZBqO1MZK_RMqEEYK_QKq0aq9BE2-I3Et9TqVknA7mGdi_SdvnSdt90m3v3f-fH7b-Rcv_ACCLq4g</recordid><startdate>20150501</startdate><enddate>20150501</enddate><creator>Kirkwood, Jobie</creator><creator>Hargreaves, David</creator><creator>O'Keefe, Simon</creator><creator>Wilson, Julie</creator><general>Oxford University Press</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>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7SC</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>5PM</scope></search><sort><creationdate>20150501</creationdate><title>Using isoelectric point to determine the pH for initial protein crystallization trials</title><author>Kirkwood, Jobie ; Hargreaves, David ; O'Keefe, Simon ; Wilson, Julie</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c543t-ae32797892e40f67961f5b0e6cbb09e5160486d315502bd7455128c2daa54f9f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Bioinformatics</topic><topic>Buffer solutions</topic><topic>Buffers</topic><topic>Crystallization</topic><topic>Estimates</topic><topic>Hydrogen-Ion Concentration</topic><topic>Isoelectric Point</topic><topic>Mathematical models</topic><topic>Original Papers</topic><topic>Proteins</topic><topic>Proteins - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kirkwood, Jobie</creatorcontrib><creatorcontrib>Hargreaves, David</creatorcontrib><creatorcontrib>O'Keefe, Simon</creatorcontrib><creatorcontrib>Wilson, Julie</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>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kirkwood, Jobie</au><au>Hargreaves, David</au><au>O'Keefe, Simon</au><au>Wilson, Julie</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Using isoelectric point to determine the pH for initial protein crystallization trials</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2015-05-01</date><risdate>2015</risdate><volume>31</volume><issue>9</issue><spage>1444</spage><epage>1451</epage><pages>1444-1451</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><eissn>1460-2059</eissn><abstract>The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.
Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.
Data used to generate models are available as Supplementary Material.
julie.wilson@york.ac.uk
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>25573921</pmid><doi>10.1093/bioinformatics/btv011</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central; Alma/SFX Local Collection |
| subjects | Bioinformatics Buffer solutions Buffers Crystallization Estimates Hydrogen-Ion Concentration Isoelectric Point Mathematical models Original Papers Proteins Proteins - chemistry |
| title | Using isoelectric point to determine the pH for initial protein crystallization trials |
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