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Ground-State Structures of Hydrated Calcium Ion Clusters From Comprehensive Genetic Algorithm Search.

ABSTRACT: We searched the lowest-energy structures of hydrated calcium ion clusters Ca²⁺(H₂O)_n (n = 10-18) in the whole potential energy surface by the comprehensive genetic algorithm (CGA). The lowest-energy structures of Ca²⁺(H₂O)_10-12 clusters show that Ca²⁺ is always surrounded by six H₂O molecules in the first shell. The number of first-shell water molecules changes from six to eight at n = 12. In the range of n = 12-18, the number of first-shell water molecules fluctuates between seven and eight, meaning that the cluster could pack the water molecules in the outer shell even though the inner shell is not full. Meanwhile, the number of water molecules in the second shell and the total hydrogen bonds increase with an increase in the cluster size. The distance between Ca²⁺ and the adjacent water molecules increases, while the average adjacent O-O distance decreases as the cluster size increases, indicating that the interaction between Ca²⁺ and the adjacent water molecules becomes weaker and the interaction between water molecules becomes stronger. The interaction energy and natural bond orbital results show that the interaction between Ca²⁺ and the water molecules is mainly derived from the interaction between Ca²⁺ and the adjacent water molecules. The charge transfer from the lone pair electron orbital of adjacent oxygen atoms to the empty orbital of Ca²⁺ plays a leading role in the interaction between Ca²⁺ and water molecules.

SUBMITTER: Shi R

PROVIDER: S-EPMC8277924 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method.

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Ground-State Structures of Hydrated Calcium Ion Clusters From Comprehensive Genetic Algorithm Search.

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