1 BUILDING A STRUCTURAL MODEL OF KCSA 16
visualized for residue His25 (Fig. 4 A). Thus we will mo del both as HSE residues.
pH- and voltage- dependent gating of KcsA. Identifying the cor-
rect protonation state of histidines might be essential in proteins
such as KcsA. This potassium channel has been shown to be acti-
vated by proton binding in the intracellular side of the channel. In
addition, although KcsA lacks a canonical voltage-sensing domain,
KcsA gating is influenced by voltage. The voltage and pH sen-
sors are likely different physical entities (Julio F. Cordero-Morales,
Luis G. Cuello, and Eduardo Perozo, Nature Structural & Molecular
Biology 13, 319–322, 2006).
9 Create the following additional graphical represe ntation in VMD:
Selection Drawing Method Coloring Method
charged and chain C Licorice ResType
10 Identify all charged residues. Look at res idues Arg27, Arg52, Arg64,
Arg89, Arg117, Arg121, and Arg122. Note that Arg117 is missing its
side chain. All arginines are loc ated in regions that are likely solvated
(Fig. 4 B). Thus we will model them as charged.
11 Look at residues Glu51, Glu71, Asp80, Glu118, and Glu120. Do you notice
something unusual?
Residues Asp80 and Glu71 are very close to each other and actually interact
through a water molecule. Likely, both residues share one proton and are not
negatively charged at the same time (Fig. 4 C). Classical molecular dynam-
ics simulations cannot acc urately describe such state. Therefore, we will model
Glu71 as a neutral amino-acid by applying the patch GLUP, as indicated below.
12 Exit VMD.
Protonation states of ionizable r esidues. It is usually desirable to
use advanced pK
a
calculations to reliably assign protonation states.
The ionization state of residues such as glutamate, aspartate, lysine,
and arginine can be extremely relevant for the function of a protein.
For instance, the protonation state of Glu71 has been shown to be
relevant for the dynamics and stability of KcsA (Simon Bern`eche
and Benoˆıt Roux, Biophysical Journal 82, 772–780, 2002).
You should have by now ten (!) files (segA.pdb, segB.pdb, segC.pdb, segD.pdb,
pot.pdb, filtwat.pdb, and crystwatA.pdb, crystwatB.pdb, crystwatC.pdb,
(30 páginas)
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