Re: [ccp4bb] Crystal Structures as Snapshots

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Crystal Structures as Snapshots
From: Jacob Keller j-keller2 {- at -} FSM {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2012-02-10

Next message:
Subject: Re: Crystal Structures as Snapshots
From: Mark Wilson mwilson13 {- at -} UNLNOTES {- dot -} UNL {- dot -} EDU
Date: 2012-02-10

Subject: Re: Crystal Structures as Snapshots
From: Jon Agirre jon {- dot -} agirre {- at -} GMAIL {- dot -} COM
Date: 2012-02-10

Hi Nat,

there are a number of viruses in which a domain swap occurs inside the
capsid, with the hinge sequence being highly conserved among their
respective families. Perhaps I'm missing your point, but I won't attribute
that kind of domain swap to any sort of crystal packing artifact.

Jon

2012/2/10 Nat Echols

> Just to clarify - I actually think the original assumption that Jacob
> posted is generally reasonable. But it needn't necessarily follow
> that the conformation we see in crystal structures is always
> representative of the solution state; given the extreme range of
> conditions in which crystals grow, I would be surprised if there
> weren't counter-examples. I'm not familiar enough with the literature
> on domain swapping (e.g. diptheria toxin) to know if any of those
> structures are crystal packing artifacts.
>
> On Fri, Feb 10, 2012 at 1:04 PM, George wrote:
> >>Packing billions of copies into a compact lattice
> > Not so compact there is 40-80% water
> >>freezing it to 100K
> > We have frozen many times protein solutions in liquid nitrogen and then
> thaw
> > and were working OK
> >> non-physiological amounts of salt and various organics
> > What is the amount of salt and osmotic pressure in the cell??
> >>non-physiological pH too
> > What is the non-physiological pH too? I am sure that some enzymes they
> are
> > not working in pH 7. Also most of the proteins they have crystallized in
> pH
> > close to 7 so I would not say non-physiological.
> >
> > George
> >
> > PS There are lots of solution NMR structures as well supporting the
> > physiological crystal structures
> >
> >
> > -----Original Message-----
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Nat
> > Echols
> > Sent: Friday, February 10, 2012 10:35 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Crystal Structures as Snapshots
> >
> > On Fri, Feb 10, 2012 at 12:29 PM, James Stroud
> wrote:
> >> How could they not be snapshots of conformations adopted in solution?
> >
> > Packing billions of copies of an irregularly-shaped protein into a
> > compact lattice and freezing it to 100K isn't necessarily
> > representative of "solution", especially when your solution contains
> > non-physiological amounts of salt and various organics (and possibly
> > non-physiological pH too).
> >
> > -Nat
> >
>

--
Dr. Jon Agirre
Postdoctoral Scientist - Protein and
Virus X-ray Crystallography Group
Biophysics Unit (CSIC-UPV/EHU)
+0034946013357

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Crystal Structures as Snapshots
From: Jacob Keller j-keller2 {- at -} FSM {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2012-02-10

Next message:
Subject: Re: Crystal Structures as Snapshots
From: Mark Wilson mwilson13 {- at -} UNLNOTES {- dot -} UNL {- dot -} EDU
Date: 2012-02-10