[ccp4bb]: Buried protonated acids - Summary of responses

[Stephen Graham <stepheng@mail.usyd.edu.au>]

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Hi CCP4-ers

Many thanks to all those who took the time to reply to my message.  It
seems like buried protonated acids do pop up from time to time in
protein structures.  As Ulrich Genick pointed out,

    "...physical chemistry is firmly on your side. The low
     dielectric constant inside a protein clearly disfavours
     deprotonation, so by default, one would expect
     a burried glutamic acid to be protonated."

Ulrich also pointed out that

    "The local pH inside the protein interior is often
     extremely different from the pH in the surrounding
     solution. Some people may even argue, that defining  
     a pH inside a protein interior makes no sense at all."

Bernard Santarsiero mentioned that

    "...ultra-high-resolution x-ray and neutron diffraction crystal
     structures ... are more reliable with hydrogen atom assignment. One
     recent structure on beta-lactamase (J.  Amer.  Chem. Soc., 124,
     6333, 2002) shows a couple of nice Asp's that are hydrogen-bonded to
     amide nitrogen atoms (A85, A131), etc.   The coords are deposited in
     the pdb also (1M40).   In this structure, one of the main claims is
     that Glu166 is protonated, even though the crystals are grown at
     pH8.0."

Randy Read pointed out that a paper has been written on this kind of
interaction: Sawyer, L & James, MN, "Carboxyl-carboxylate interactions
in proteins", Nature 295:79-80 (1982).  Unfortunately I will have to
wail 'til Monday to trundle down to the library and check this one out
since Nature does not have a complete online archive!

Frank Vondelft suggested that I look at the UCL side chain atlas
(http://www.biochem.ucl.ac.uk/bsm/sidechains/).  Unfortunately its
archive holds only sidechain-sidechain interactions, not
sidechain-backbone interactions.  None the less, an interesting site.

Lastly, here is a list of people who sent me literature examples and the
examples which they quoted:

Lionel Mourey:
    P. Swarén et al. (1995). Structure, 3(6), 603-613

Ulrich K. Genick:
    Borgstahl GE, Williams DR, Getzoff ED.  1.4 A structure of
    photoactive yellow protein, a cytosolic photoreceptor: unusual fold,
    active site, and chromophore.  Biochemistry. 1995 May
    16;34(19):6278-87.

    Genick UK, Soltis SM, Kuhn P, Canestrelli IL, Getzoff ED.  Structure
    at 0.85 A resolution of an early protein photocycle
    intermediate.Nature. 1998 Mar 12;392(6672):206-9.

    Demchuk E, Genick UK, Woo TT, Getzoff ED, Bashford D.  Protonation
    states and pH titration in the photocycle of photoactive yellow
    protein. Biochemistry. 2000 Feb 8;39(5):1100-13.

Bernard Santarsiero:
    J. Amer. Chem. Soc., 124, 5333, 2002

Jean-Philippe Cartailler:
    J. Mol. Biol. (1999) Structure of Bacteriorhodopsin at 1.55 A
    resolution. 291, 899-911

Zac Wood:
    Wood ZA, Poole LB, Karplus PA. Biochemistry. 2001 Apr
    3;40(13):3900-11, "Structure of intact AhpF reveals a mirrored
    thioredoxin-like active site and implies large domain rotations
    during catalysis".

Rik Wierenga:
    prot engin 12  (1999) 243-250.
    ejb 267 (2000) 2516-2524.

Christopher Davies:
    Davies et al (1994) Structure 4, 55-66

Christian Jelsch:
    Jelsch et al., Proteins, 16, 364-383.  1993.

Thanks again to all who replied,

Stephen

This one time, at band camp, Stephen Graham said:
> ***  For details on how to be removed from this list visit the  ***
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> 
> Hey CCP4ers,
> 
> Apologies for the not-directly-CCP4-related question.  I am working on a
> structure at 2.4 A resolution where I see what I believe to be a
> protonated acid buried in the core of the protein.  Specifically, I have
> an Asp residue whose OD2 is 2.93 A from an amide nitrogen (forming a
> nice H-bond) and whose OD1 is 2.56 A from a carbonyl oxygen.  All
> residues mentioned are very well ordered (low Bs) and are well defined
> in electron density.  The pH of the crystallisation conditions is 8.5.
> 
> >From my understanding such protonated acids are not especially unusual.
> I have, however, been unable to find any literature references for such
> buried protonated acids.  MEDLINE and the Acta Cryst. archives have not
> proved allies in my search.  Can anyone point me towards examples of
> such buried protonated acids in the literature?
> 
> Thanks in advance
> 
> Stephen
> 
> -- 
> Stephen Graham
> PhD candidate and nasty sysadmin
> Crystallography Group
> School of Molecular and Microbial Biosciences
> Building G08
> University of Sydney
> New South Wales, 2006
> Australia
> Ph: +61 2 9351 8197
> Fax: +61 2 9351 4726

-- 
Stephen Graham
PhD candidate and nasty sysadmin
Crystallography Group
School of Molecular and Microbial Biosciences
Building G08
University of Sydney
New South Wales, 2006
Australia
Ph: +61 2 9351 8197
Fax: +61 2 9351 4726