Model proteins molecular structure

M. Karplus, Molecular Dynamics Applications to Proteins , ed. J. L. Rivail, Modelling of Molecular Structures and Properties , Elsevier Science Publishers, Amsterdam, 1990, pp. 427-461. 

Mosimann S, S Meleshko and M N G Jones 1995. A Critical Assessment of Comparative Molecular Modeling of Tertiary Structures of Proteins. Proteins Structure, Function and Genetics 23 301-317. 

S Mosimann, R Meleshko, MNG lames. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 23 301-317, 1995. 

AL Delcher, S Kasif, HR Goldberg, WH Hsu. Protein secondary structure modelling with probabilistic networks. Intelligent Systems m Molecular Biology 1 109-117, 1993. 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

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