MOLECULAR REPLACEMENT FOR MULTI-DOMAIN PROTEINS

What is Molecular Replacement?

Given a known single-domain protein structure, one can often obtain a good estimate of the orientation of an unknow (but homologous) structure in its crystallographic unit cell by performing an orientational match of Patterson functions of the known and unknown proteins. Finding this orientation is often the first stem in structure determination from crystallographic data. This is followed by searching for the position of each copy in the unit cell. This method is widely used, but often fails for multidomain proteins. For more information, please click here [publication].

MR for Multidomain Proteins

Figures: Illustrations of the closed form and open form of Lactoferrin (PDB code: ILFG and ILFH). One domain rotated to open binding site

Procedures

1. Finding the orientation of each seperated domain by conventional MR program (AMoRe, MolRep)
2. Calculate the relative orientation between domains in the target crystal
3. Morph the template conformation into the candidate conformations which satisfy the relative rotations by using iterative NMA
4. Apply the candidate conformation into MR program to calculate the translation function in the target crystal

Iterative NMA (iNMA)

• Morphing the template conformation into candidate conformations
• Iterative procedures calculating normal mode from Elastic Network Model
• Cost function: relative rotation between domains
• Elastic network minimization is used in order to guarantee the geometric constraints of conformation
• Reconstruct the backbone atoms or side-chains by using MaxSprout program and Deepview

Figures: Flowchart of iNMA

MR Results

Figures: Morphing 1URP into 2DRI

Figures: (left) Crystal packing of the target (2DRI) and (right) Crystal packing of the fianl candidate morphed 1URP by using iNMA

Figures: Morphing 1LFG into 1LFH