Protein structures energy

Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F. Statistical mechanics and molecular dynamics The calculation of free energy, in Molecular Dynamics and Protein Structure, J. Hermans, ed.. Polycrystal Book Service, PO Box 27, Western Springs, 111., USA, (1985) 43-46. 

Bryant S H and C E Lawrence 1993. An Empirical Energy Function for Threading Protein Sequences Through the Folding Motif. Proteins Structure, Punction and Genetics 16 92-112. 

Bryngelson J D, J N Onuchic, N D Socci and P G Wolynes 1995. Funnels, Pathways, and the Energy Landscape of Protein Folding A Synthesis. Proteins Structure, Function and Genetics 21 167-195. 

Boresch S, G Archontis and M Karplus 1994. Free Energy Simulations The Meaning of the Indi-. id Contributions from a Component. Analysis. Proteins Structure, Function and Gau tics 20 25-33. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

Miyamoto S and P A Kollman 1993a. Absolute and Relative Binding Tree Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Using Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16 226-245. 

Most potential energy surfaces are extremely complex. Fiber and Karplus analyzed a 300 psec molecular dynamics trajectory of the protein myoglobin. They estimate that 2000 thermally accessible minima exist near the native protein structure. The total number of conformations is even larger. Dill derived a formula to calculate the upper bound of thermally accessible conformations in a protein. Using this formula, a protein of 150 residues (the approx-... 

Molecular dynamics simulations of proteins often begin with a known structure (such as an X-ray diffraction structure) that you want to maintain during equilibration. Since the solvent may contain high energy hot spots, equilibration of the protein and solvent at the same time can change the protein conformation. To avoid this, select only the water molecules and run a molecular dynamics equilibration. This relaxes the water while fixing the protein structure. Then deselect the water and equilibrate the whole system. 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

F Melo, E Feytmans. Assessing protein structures with a non-local atomic interaction energy. JMol Biol 277 1141-1152, 1998. 

DM Standley, JR Gunn, RA Friesner, AE McDermott. Tertiary structure prediction of mixed alpha/beta proteins via energy minimization. Proteins 33 240-252, 1998. 

Several different kinds of noncovalent interactions are of vital importance in protein structure. Hydrogen bonds, hydrophobic interactions, electrostatic bonds, and van der Waals forces are all noncovalent in nature, yet are extremely important influences on protein conformations. The stabilization free energies afforded by each of these interactions may be highly dependent on the local environment within the protein, but certain generalizations can still be made. 

FIGURE 1.4 Increasing levels of protein structure. A protein has a given amino acid sequence to make peptide chains. These adopt a 3D structure according to the free energy of the system. Receptor function can change with changes in tertiary or quaternary structure. 

Electrostatic stabilization, 181, 195,225-228 Empirical valence bond model, see Valence bond model, empirical Energy minimization methods, 114-117 computer programs for, 128-132 convergence of, 115 local vr. overall minima, 116-117 use in protein structure determination,... 

Transition from the high-energy phosphoform E]P[3Na] to the K-sensitive E2P[2Na] of Na,K-ATPase are accompanied by conformational transitions in protein structure and changes of the capacity and orientation of cation sites. In the Ej form of Na,K-ATPase, the exposure of Chys (Leu ) and Trys (Arg ) to cleavage reflects that the cation sites of the phosphoprotein are in a conformation oriented towards the cytoplasm with a capacity for occlusion of three Na ions. The E2 form... 

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