5 April 2004 Self-organization of Cro protein: a molecular dynamics study
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Abstract
In this contribution, we report on a study of the self-organization of Cro protein. The process is computer simulated by the method of molecular dynamics. We investigated folding of the Cro regulatory protein of bacteriophage λ. Spontaneous transition of α-spiral structure into a globule was observed. In some cases the self-organization was similar to that obtained earlier for simple organic polymers and proteins. We have developed a graphical way of analysis of three-dimensional protein structures that transforms three-dimensional structures into quasi two-dimensional ones. With the help of this method we have found that the folding consists of three stages which incorporate formation of transverse waves in an elongated helix rectilinear structure taken as an initial conformation, compression and collapse of these waves, and reptile motion of helices in regions with bad local order or search of a native conformation.
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Maria A. Vorobyeva, Maria A. Vorobyeva, Alexander I. Melker, Alexander I. Melker, Sergey A. Mendeleev, Sergey A. Mendeleev, "Self-organization of Cro protein: a molecular dynamics study", Proc. SPIE 5400, Seventh International Workshop on Nondestructive Testing and Computer Simulations in Science and Engineering, (5 April 2004); doi: 10.1117/12.555444; https://doi.org/10.1117/12.555444
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