AMBER Archive (2009)

Subject: [AMBER] What is the Optimum Ph for solvating a protein

From: Ashish Runthala (
Date: Sun Sep 13 2009 - 08:08:40 CDT

As per the given literature, pH 7.0 is considered and we neutralize
the system before any further analysis.
So now explain me, if we consider the system neutralized, why the
charged side chains of amino acids exist in nature. Sometimes i found
the drugs also interacting at a certain specific docking distance with
these side chains. If that is so, why we force neutral system.
If i need to change pH of the protein system. What should i do to
attain it. I need to equilibrate my protein at pH 8.25

Thanks in advance,

Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

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