Penalized multidimensional fitting for protein movement detection

ABSTRACT

The three-dimensional structure of a given protein can take different conformations depending upon the reaction it undergoes and its substrate/cofactor/partners binding state. Various methods exist to study these conformational changes but only one, called DynDom, is clearly focused on movement detection. An alternative method is proposed, making use of multivariate data analysis, called ‘penalized Multidimensional Fitting (penalized MDF)’ based on penalized movements of points in order to approach the distances between points after movement to the distances given by the reference matrix. The objective is to detect the amino acids that undergo an important movement by fitting the distances of one conformation to the distances of the second one by modifying only the coordinates of the first one. This method is applied to three different proteins.

KEYWORDS:

• Multidimensional analysis
• data analysis
• conformational changes
• ligand binding
• penalization
• optimization

AMS SUBJECT CLASSIFICATION:

• 62P10
• 62H99

Disclosure statement

No potential conflict of interest was reported by the authors.