Fwd: STRIDE Question from article "Interpeptide interactions induce helix to strand structural transition in Abeta peptides"

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Tue Mar 23 2010 - 01:34:47 CDT

---------- Forwarded message ----------
From: Aditya Ranganathan <aditya.sia_at_gmail.com>
Date: Tue, Mar 23, 2010 at 12:03 PM
Subject: Regarding article "Interpeptide interactions induce helix to strand
structural transition in Abeta peptides"
To: klimov_at_glue.umd.edu

Hello,

Iam a research student from the Indian Institute of Technology, Bombay,
India. We, in our lab are trying to study inter peptide interaction between
ACTH and Beta Endorphin (human) and are interested the know the Random Coil
to Beta Sheet transforming tendency of ACTH in presence of Beta Endorphin. I
read your paper titled "Interpeptide interactions induce helix to strand
structural transition in Abeta peptides" and came across the secondary
structure assignment method which you`ve employed in that paper defined
using Phi and Psi angles and the Ramachandran Plot.
Ours is a simulation where we are looking at whether ACTH forms an ordered
structure with 2 Beta Endorphin with time and whether it shows Beta strand
tendencies. I used the Secondary Structure tool in VMD which assigns
secondary structure according to STRIDE. However most part of it is being
still displayed as Turns or Coils and as per your paper "STRIDE
underestimates extended strand like structures by assigning them to coils
and turns". I chedked the Ramachandran plot of my structure and according to
the Ramachandran plot, many more residues fall in the Beta Strand allowed
regions of the plot than STRIDE has assigned.

I`m now confused as to which of the two I should go by in this case to
define the secondary structure.

Thanks

Srivastav Ranganathan (Aditya)
Junior Research Assistant
IIT-Bombay,Powai
Mumbai-400076
India
Phone : 91-09967556626

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