Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase

• Published in: Journal of molecular biology 2005-09, Vol.352 (4), p.807-822
• Main Authors: Maragakis, Paul, Karplus, Martin
• Format: Article
• Language: English
• Subjects: adenylate kinase; Adenylate Kinase - chemistry; conformational change pathway; elastic network; Escherichia coli; Escherichia coli - enzymology; Escherichia coli Proteins - chemistry; minimum energy path; Models, Molecular; Models, Theoretical; Molecular Sequence Data; Protein Conformation; Statistics as Topic
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.07.031

The plastic network model (PNM) is used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. In this model, the energy basins corresponding to known conformers are connected at their lowest common energies. The results are used to evaluate and analyze the minimal energy pathways between these basins. The open to closed transition analysis provides an identification of hinges that is in agreement with the existing definitions based on the available X-ray structures. The elastic energy distribution and the C α pseudo-dihedral variation provide similar information on these hinges. The ensemble of the 45 published structures for this protein and closely related proteins is shown to always be within 3.0 Å of the pathway, which corresponds to a conformational change between two end structures that differ by a C α-atom root-mean-squared deviation of 7.1 Å.