Protein 2 loops

The multisubstate approach requires initially identifying all important substates, a difficult and expensive operation. In cases of moderate complexity (e.g., a nine-residue protein loop), systematic searching and clustering have been used [39,66]. For larger systems, methods are still being developed. 

HWT van Vlijmen, M Karplus. PDB-based protein loop prediction Parameters for selection and methods for optimization. I Mol Biol 267 975-1001, 1997. 

B Oliva, PA Bates, E Querol, LX Aviles, MIL Sternberg. An automated classification of the structure of protein loops. I Mol Biol 266 814-830, 1997. 

I Wojcik, I-P Mornon, I Chomilier. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. I Mol Biol 289 1469-1490, 1999. 

V Collura, I Higo, I Gamier. Modeling of protein loops by simulated annealing. Protein Sci 2 1502-1510, 1993. 

Q Zheng, R Rosenfeld, S Vajda, C DeLisi. Determining protein loop conformation using scahng-relaxation techniques. Protein Sci 2 1242-1248, 1993. 

Q Zheng, R Rosenfeld, C DeLisi, DJ Kyle. Multiple copy sampling in protein loop modeling Computational efficiency and sensitivity to dihedral angle perturbations. Protein Sci 3 493-506, 1994. 

The main advantage of NMR spectroscopy is its use with proteins in solution. In consequence, rather than obtaining a single three-dimensional structure of the protein, the final result for an NMR structure is a set of more or less overlying structures which fulfill the criteria and constraints given particularly by the NOEs. Typically, flexibly oriented protein loops appear as largely diverging structures in this part of the protein. Likewise, two distinct local conformations of the protein are represented by two differentiated populations of NMR structures. Conformational dynamics are observable on different time scales. The rates of equilibration of two (or more) substructures can be calculated from analysis of the line shape of the resonances and from spin relaxation times Tj and T2, respectively. 

Kolodny, R., Guibas, L., Levitt, M., Koehl, P. Inverse kinematics in biology the protein loop closure problem. Int. J. Robot. Res. 2005, 24, 151-63. 

Conversion of potentially active gene to active gene requires binding of regulatory w proteins, looping of chromosome, and binding of polymerase. 

Gerstein, M. and C. Chothia (1991). Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. J. Mol. Biol. 220 133-149. 

We have tested the loop prediction algorithms on two sets of protein loops of known structure (see [101]). The first set is composed of the 57 nine-residue loops that were originally compiled by Fiser et al. [126] and by Xiang et al. [127]. The 35 13-residue loop set is the same as the one investigated by Zhu et al. [124],... 

One example is in the enzyme dihydrofolate reductase, where replacement of Gly- 120 to valine disrupts the internal motion of a protein loop, as Ulnstrated in Fig. 18, which leads to a 500-fold reduction in rate this rednction in rate implies that internal motion is involved in catalysis (14). 

Vajda S, Camacho CJ. Protein-protein docking is the glass half-full or half-empty Trends Biotechnol. 2004 22 110-116. Derreumaux P, Schlick T. The loop opening/closing motion of the enzyme triosephosphate isomerase. Biophys. J. 1998 74 72-81. Gerstein M, Chothia C. Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase. J. Mol Biol 1991 220 133-149. 

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