Using known substructures in protein model building and crystallography.

Jones, T. Alwyn; Thirup, Søren

doi:10.1002/j.1460-2075.1986.tb04287.x

Cited by 784 publications

(412 citation statements)

References 29 publications

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“…4,10,11 Another family of comparative methods relies on approximate positions of conserved atoms from the templates to calculate the coordinates of other atoms. 12,13 A third group of methods uses either distance geometry or optimization techniques to satisfy spatial restraints obtained from the sequence-template alignment. [14][15][16] There are also many methods that specialize in the modeling of loops [17][18][19] and side chains 20,21 within the restrained environment provided by the rest of the structure.…”

Section: Comparative Modeling and Threadingmentioning

confidence: 99%

Evolution and Physics in Comparative Protein Structure Modeling

et al. 2002

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From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

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Section: Comparative Modeling and Threadingmentioning

confidence: 99%

Evolution and Physics in Comparative Protein Structure Modeling

et al. 2002

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“…Loop regions were then constructed by selecting a fragment for modeling loop regions from the general protein database (Jones and Thirup 1986;Claessens et al 1989). The force field for simulation of proteins (Weiner et al 1984(Weiner et al , 1986) was employed in the minimization steps to optimize the geometry of a molecule.…”

Section: Immunocytochemical Analysismentioning

confidence: 99%

Molecular and structural studies of Japanese patients with sialidosis type 1

et al. 2000

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To gain insight into the pathogenesis of sialidosis type 1, we performed molecular investigations of two unrelated Japanese patients. Both of them are compound heterozygotes for base substitutions of 649 G-to-A and 727 G-to-A, which result in amino acid alterations V217M and G243R, respectively. Using homology modeling, the structure of human lysosomal neuraminidase was constructed and the structural changes caused by these missense mutations were deduced. The predicted change due to V217M was smaller than that caused by G243R, the latter resulting in a drastic, widespread alteration. The overexpressed gene products containing these mutations had the same molecular weight as that of the wild type, although the amounts of the products were moderately decreased. A biochemical study demonstrated that the expressed neuraminidase containing a V217M mutation was partly transported to lysosomes and showed residual enzyme activity, although a G243R mutant was retained in the endoplasmic reticulum/Golgi area and had completely lost the enzyme activity. Considering the data, we surmise that the V217M substitution may be closely associated with the phenotype of sialidosis type 1 with a late onset and moderate clinical course.

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“…Indeed, if the sequence of a protein with an unknown structure can be related to one with a known architecture, the main chain folding for the latter provides a valid starting point for the structural modelling of the former (e.g. [1][2][3]). …”

Section: Introductionmentioning

confidence: 99%

Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences

et al. 1987

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A new method for comparing and aligning protein sequences is described. This method, hydrophobic cluster analysis (HCA), relies upon a two-dimensional (2D) representation of the sequences. Hydrophobic clusters are determined in this 2D pattern and then used for the sequence comparisons. The method does not require powerful computer resources and can deal with distantly related proteins, even if no 3D data are available. This is illustrated in the present report by a comparison of human haemoglobin with leghaemoglobin, a comparison of the two domains of liver rhodanese (thiosulphate sulphurtransferase) and a comparison of plastocyanin and azurin.

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Using known substructures in protein model building and crystallography.

Cited by 784 publications

References 29 publications

Evolution and Physics in Comparative Protein Structure Modeling

Evolution and Physics in Comparative Protein Structure Modeling

Molecular and structural studies of Japanese patients with sialidosis type 1

Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences

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