[ccp4bb] inflluence of pH for crystallization on protein 3-D structure
Acoot You may be interested in some data-mining that we did a few years ago http://www.douglas.co.uk/PDB_data.htm#Acid-base We didn't see any obvious correlations On 28 October 2012 03:00, Acoot Brett acootbr...@yahoo.com wrote: Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure
An example for how crystallization at non-physiological pH (and non-physiological concentrations and non-physiological environmental) may influence behavior of the protein is the Botulinum A LC protease. Under normal conditions (upon endocytosis of a few molecules at best into the nerve cell), it works like a canonical serine protease, but at pH 4.6 it cleaves itself in a non-canonical fashion, i.e. with a loop resembling the target peptide running opposite direction. Later isoform structures solved at neutral pH showed normal, canonical protease activity. http://www.ruppweb.org/cvs/br/Segelke_2004_PNAS_botulinum_neurotoxin.pdf BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Acoot Brett Sent: Saturday, October 27, 2012 8:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot
Re: [ccp4bb] inflluence of pH for crystallization on protein 3-D structure
Hi Acoot, Here are some examples you can look at: PDB: 1X0I (crystal structure of bacteriorhodopsin (acid blue form) at pH 2) PDB: 1X0K (crystal structure of bacteriorhodopsin at pH 10) PDB: 2W2E (crystal structure of aquaporin at pH 3.5) PDB: 1YMG (crystal structure of aquaporin at pH 10) People are aware of course of the effect of pH on the structure and they always deposit many PDBs when they have different crystal forms/bound molecules, or pHs. The difference sometimes can be large that they will do another publication/study like when getting the different structure at a different pH. I can't remember the details but a virus protein crystal structure was once crystallized at both pH 4 and pH 7 which gave totally unrelated structures. Functional studies are important before the interpretation of the structure. Regards Toufic El Arnaout Membrane Structural and Functional Biology Group Trinity College Dublin On Sun, Oct 28, 2012 at 3:00 AM, Acoot Brett acootbr...@yahoo.com wrote: Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot
[ccp4bb] inflluence of pH for crystallization on protein 3-D structure
Dear All, A protein crystal can be got at pH 5 or 8, or a pH with much extreme value. What will be the relatively extreme pH value to get the crystal on the protein structure solved based on the crystal got? I mean usually we regard the physiological pH as 7. If a crystal was got at pH 5, the structure solved may be different from the protein structure at pH 7. But it seems there is rarely analysis on the discrepancy of the protein structures when publishing 3-D structure with the protein crystal got at relatively extreme pH. I am looking forward to getting your comment on it. Cheers, Acoot
