Loop closure

A solution leading to a successful algorithm was recently found for the folding of ribonucleic acid (RNA) [36], Natural RNA polymers (figure C2.14.1) are mainly made up from four different bases . A, C, G and U. As with DNA, multiple hydrogen bonding favours the fonnation of G-C and A-U pairs [16, 37, 38] which leads to the appearance of certain characteristic stmctures. Loop closure is considered to be the most important folding event. 

V (the potential) is identified with the enthalpy, i.e. the number n of base pairings (contacts), and T corresponds to the entropy. At each stage in the folding process, as many as possible new favourable intramolecular interactions are fonned, while minimizing the loss of confonnational freedom (the principle of sequential minimization of entropy loss, SMEL). The entropy loss associated with loop closure is (and the rate of loop closure exp... 

A possible explanation for the existence of a minimum value of relative pressure for loop closure was hinted at by Schofield in 1948, who suggested... 

On a lattice, so-called crankshaft moves are trivial implementations of concerted rotations [77]. They have been generalized to the off-lattice case [78] for a simplified protein model. For concerted rotation algorithms that allow conformational changes in the entire stretch, a discrete space of solutions arises when the number of constraints is exactly matched to the available degrees of freedom. The much-cited work by Go and Scheraga [79] formulates the loop-closure problem as a set of algebraic equations for six unknowns reducible... 

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. 

Kiselev, using the above equation by graphical integration of the isotherm between the limits of saturation and hysteresis loop closure, was able to calculate surface areas for wide-pore samples in good agreement with BET measured areas. For micropores, the absence of hysteresis at the low-pressure end of the isotherm indicates that only adsorption and not condensation occurs, thereby rendering Kiselev s method inapplicable. 

A model of the randomly colling form of polylrll) based on minimum-energy conformers of UpU is described. The blend of conformers is chosen to fit the C—C rotational populations derived in NMR studies of UpU and poly(rU) and to match the experimental unperturbed dimensions of the poly(rU) chain. In addition, estimates of loop closure based on the model are comparable to the sizes of loops most frequently seen In the model oligonucleotides. Approximately 60% of the conformers constituting the model are characterized by stacked, extended C2 -endo ra cmy = tg g+ rotations. 

N 124 "Loop Formation in Polynucleotide Chains. I. Theory of Hairpin Loop Closure"... 

A key structural and mechanistic feature of lactate and malate dehydrogenases is the active site loop, residues 98-110 of the lactate enzyme, which was seen in the crystal structure to close over the reagents in the ternary complex.49,50 The loop has two functions it carries Arg-109, which helps to stabilize the transition state during hydride transfer and contacts around 101-103 are the main determinants of specificity. Tryptophan residues were placed in various parts of lactate dehydrogenase to monitor conformational changes during catalysis.54,59,60 Loop closure is the slowest of the motions. 

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. 

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. 

For both minimization procedures described above the loop closure occurs identically as follows the peptide bond atoms located at both extremities of a loop were allowed to move during the minimizations (even when only side chains were optimized). Only four atoms per extremity was needed for loop closure because of the restricted distances between N and C termini in the establishment of the database (Pellequer Chen, 1996). 

Two ways of optimizing CDR modeled loops were tested (1) only the side chains of the loops were minimized, and (2) all atoms of loops were minimized. In the first case, the backbone was kept fixed in the original loop conformation. In the second case, all atoms were minimized in order to obtain a "clash-free" loop conformation. To reduce computational requirements, only a subset of the lowest conformational free energy loops (<1500 kcal/mol) from (1) were optimized in (2), see below. Loop closure occurs identically in both approaches and therefore does not contribute to the energy difference observed between them. Modeled loops were compared with the native loops treated with identical minimization procedures. 

Joore L, Wortel N, and Bronold N. MBR in water loop closure concepts in Dutch recycled paper mills—from pilot towards full-scale installations. Pap. Techn. 2001 42(7) 27-36. 

Yeh, I., Plummer, G. Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J. Am. Chem. Soc. 2002, 124, 6563-8. 

Database Database of 81 8 gaps in BPTI, Loop closure ... 

Q. Zheng, D. J. Kyle. Accuracy and reliability of the scaling-relaxation method for loop closure An evaluation based on extensive and multiple copy conformational samplings. Proteins. 1996, 24, 209-217. 

N. S. Sampson and J. R. Knowles, Biochemistry, 31, 8482 (1992). Segmental Movement Definition of the Structural Requirements for Loop Closure in Catalysis by Triose Phosphate Isomerase. 

Soybean Beta-amylase a-Side Water866 is found II-bondedto OE2 of Glu.380 (the nucleophile), to the O atom of Asn381, and to C-l of the reaction intermediate. Loop closure on bound substrate shields the Glul86 (acid catalyst) region and all potentially reactive atoms from solvent.101... 

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