Hi Alexandra,
the answers are in these papers and references mentioned in these papers
(list below is of course incomplete, but following the references inside
of these papers will give you the full picture):
# Jiang, J.-S. & Brunger, A. T. (1994). J. Mol. Biol. 243, 100-115.
"Protein hydrat
Hi everyone:
Can someone enlighten me as to the difference between "simple" scaling
and "Babinet scaling" in Refmac? It seems to me that Babinet scaling
is more similar to what is employed in CNS for bulk solvent correction
(Ksolv, Bsolv search). Is that correct? Would you recommend the
B
Dear All,
I was trying to upload a refmac-generated deposit file to PDB Autdep but
it says the format is invalid. So I opened the file and have a look.
In it I saw a number of lines with ... which I suspect was the
cause of error. It looks like it is corrupted. Does anyone know why it
hap
James,
I think you need to be a little more specific about what you want to
calculate. Keq for a reaction A <=> B will not change with an enzyme
mutation as the thermodynamic relationships between the reactants and
products do not change. As a catalyst, the enzyme impacts only the
free
This is absolutely correct. For many enzymes, Km
is a conflation of many rate constants in the chemical mechanism. You
would have to know for certain, based on prior mechanistic work, that
all steps subsequent to substrate binding are slow enough for the
experimentally measured Km to approximat
Km is the amount of substrate needed to get the enzyme to half-maximum
velocity. So if the brain enzyme needs 10 times less substrate to reach
half-maximum velocity, you would see the apparent Km go down from 25, not up.
Any undergrad biochemistry text will have all this stuff in it.
Or am I d
Dear James:
The problem is that the equation is for an equilibrium constant, and Km is not
one. Kd is one. If you can measure Kd, what you describe I think is fine. If
you are measuring Km, you have to find a way of justifying the Km ~ Kd
approximation, which usually is only safe for enzyme
James-
It's:
lnKd = deltaH- RT(deltaS)
As for Km ~ Kd, here be dragons...Km values cannot be treated as the Kd of a
complex because dissociation of a catalytic complex has two potential fates,
one that is denoted by a rate constant that is correlated to turnover (so,
the forward reaction leading t
Dear All,
Sorry for the non-ccp4 query.
I have solved a crystal structure of an enzyme and woring on its biochemical
aspect. We have a mutant of this enzyme and we are comparing some
thermodynamic parameters of this enzyme with mutant( lke delH and delS,
delG). we have done the expt at different te
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Hi all
I'm having some trouble creating a complete mmcif file for deposition
using the harvesting manager. It does not appear to be able to read the
files I would like to input (pdb files, mmcif, log files etc). It gives
an error: "can't read "ext": no such variable". Should I change the
exten
Marie-Hélène,
If you haven't done so I suggest trying the very simple precautions described
in this paper:
An improved protocol for rapid freezing of protein samples for long-term
storage.
Deng J. et al.
Acta Cryst. (2004). D60, 203-204
Has worked very well for me in a similar case.
Good luck
T
You might consider trehalose as a substitute for glycerol.
Cheers,
Roger Rowlett
On 11/18/09, LEDU Marie-Helene 16 wrote:
> Hello,
>
> Sorry for the unrelated question.
> We encounter important storage problem of our favorite protein.
> We can not freeze it without a lost of 50 to 90 %, and
Hmm,
You can try to precipitate it with AmmSO4 and keep it as a suspension at 4C.
Flip
LEDU Marie-Helene 16 wrote:
Hello,
Sorry for the unrelated question.
We encounter important storage problem of our favorite protein.
We can not freeze it without a lost of 50 to 90 %, and can not use g
Hello,
Sorry for the unrelated question.
We encounter important storage problem of our favorite protein.
We can not freeze it without a lost of 50 to 90 %, and can not use glycerol
without precipitation.
Would anybody have suggestions or references that could help us ?
Thanks a lot in advance.
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