Properties of proteins: Difference between revisions

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→‎Ideal metal bond distances

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-== Ideal metal bond distances ==
+== Ideal metal coordination and bond distances ==
-* classic paper: Harding, M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]
+* classic papers: Harding, M.M. (1999) [http://journals.iucr.org/d/issues/1999/08/00/ad0073/index.html The geometry of metal-ligand interactions relevant to proteins]; (2004) [https://doi.org/10.1107/S0907444904004081 The architecture of metal coordination groups in proteins]. The latter has supporting information: zip archive of the website on architecture of metal coordination groups in proteins, and PDFs containing additional tables.
-* webservice (2006) http://tanna.bch.ed.ac.uk
+* [http://web.archive.org/web/20161031170012/http://tanna.bch.ed.ac.uk/ 2016 archive of original website set up by M. Harding]; MESPEUS database (successor website but also now offline:) [http://web.archive.org/web/20160901002225/http://mespeus.bch.ed.ac.uk/MESPEUS_10/ 2016 archive of website]
-* database (2008) http://eduliss.bch.ed.ac.uk/MESPEUS/
+* [http://metalweb.cerm.unifi.it/ MetalPDB]
+* [https://csgid.org/metal_sites Check my metal]
 == Distinguishing ions from waters ==
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 that are close to each other should not have an occupancy sum greater
 than unity.
+Further possibilities:
+* From the Phenix package, try: mmtbx.water_screen model.pdb data.mtz elements=NA,K
+* WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF (http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl )
 == Melting point ==
-Thermofluor is a fluorescence-based thermal stability assay. From [http://www.uni-leipzig.de/~straeter/newsletter/images/letter_0310/thermofluor.pdf]: The experiment  is easy  to perform and  requires no prior knowledge of  the protein properties. Every standard real‐time PCR machine – available in many research labs – is suitable
+Thermofluor is a fluorescence-based thermal stability assay. From [http://www.uni-leipzig.de/~straeter/newsletter/images/letter_0310/thermofluor.pdf]: The experiment is easy to perform and requires no prior knowledge of  the protein properties. Every standard real-time PCR machine available in many research labs is suitable to  perform  this  high‐throughput  experiment in a short  time (1‐2  hours). Only relatively little protein (500 µl of protein at 1‐2  mg/ml for a 96‐well experiment) and a dye (e.g. SYPRO® Orange, Invitrogen) are required. Proteins containing prosthetic groups (e.g. FAD) may not even require  an  external  fluorophore  if  the  intrinsic  signal  can  be  used  during  the  Thermofluor experiment.  For  FAD‐containing  proteins  this method  has  been  termed  ThermoFAD.
-to  perform  this  high‐throughput  experiment  in  a  short  time  (1‐2  hours). Only  relatively  little
-protein  (500  µl  of  protein  at  1‐2  mg/ml  for  a  96‐well  experiment)  and  a  dye  (e.g.  SYPRO® Orange, Invitrogen) are required. Proteins containing prosthetic groups (e.g. FAD) may not even require  an  external  fluorophore  if  the  intrinsic  signal  can  be  used  during  the  Thermofluor experiment.  For  FAD‐containing  proteins  this method  has  been  termed  ThermoFAD.
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