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Conservation of the conformation of the porphyrin macrocycle in hemoproteins
- Biophys. J
, 1998
"... ABSTRACT The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D4h-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these ort ..."
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ABSTRACT The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D4h-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these orthogonal displacements. The x-ray crystal structures of the heme groups are described within experimental error, using the set composed of only the lowest frequency normal coordinate of each out-of-plane symmetry type. That is, the distortion is accurately simulated by a linear combination of these orthonormal deformations, which include saddling (B2u), ruffling (B1u), doming (A2u), waving (Eg), and propellering (A1u). For example, orthonormal structural decomposition of the hemes in deoxymyoglobins reveals a predominantly dom heme deformation combined with a smaller wav(y) deformation. Generally, the heme conformation is remarkably similar for proteins from different species. For cytochromes c, the conformation is conserved as long as the amino acids between the cysteine linkages to the heme are homologous. Differences occur if this short segment varies in the number or type of residues, suggesting that this small segment causes the nonplanar distortion. Some noncovalently linked hemes like those in the peroxidases also have highly conserved characteristic distortions. Conservation occurs even for some proteins with a large natural variation in the amino acid sequence.
Conservation of the Conformation of the Porphyrin Macrocycle in Hemoproteins
"... ABSTRACT The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D4h-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these ort ..."
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ABSTRACT The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D4h-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these orthogonal displacements. The x-ray crystal structures of the heme groups are described within experimental error, using the set composed of only the lowest frequency normal coordinate of each out-of-plane symmetry type. That is, the distortion is accurately simulated by a linear combination of these orthonormal deformations, which include saddling (B2u), ruffling (B1u), doming (A2u), waving (Eg), and propellering (A1u). For example, orthonormal structural decomposition of the hemes in deoxymyoglobins reveals a predominantly dom heme deformation combined with a smaller wav(y) deformation. Generally, the heme conformation is remarkably similar for proteins from different species. For cytochromes c, the conformation is conserved as long as the amino acids between the cysteine linkages to the heme are homologous. Differences occur if this short segment varies in the number or type of residues, suggesting that this small segment causes the nonplanar distortion. Some noncovalently linked hemes like those in the peroxidases also have highly conserved characteristic distortions. Conservation occurs even for some proteins with a large natural variation in the amino acid sequence.
Exploring the potential of template-based modelling
"... Motivation: Template-based modelling can approximate the unknown structure of a target protein using an homologous template structure. The core of the resulting prediction then comprises the structural regions conserved between template and target. Target prediction could be improved by rigidly repo ..."
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Motivation: Template-based modelling can approximate the unknown structure of a target protein using an homologous template structure. The core of the resulting prediction then comprises the structural regions conserved between template and target. Target prediction could be improved by rigidly repositioning such single template, structurally conserved fragment regions. The purpose of this paper is to quantify the extent to which such improvements are possible and to relate this extent to properties of the target, the template and their alignment. Results: The improvement in accuracy achievable when rigid fragments from a single template are optimally positioned was calculated using structure pairs from the HOMSTRAD database, as well as CASP7 and CASP8 target/best template pairs. Over the union of the structurally conserved regions, improvements of 0.7A ̊ in RMSD and 6 % in GDT HA were commonly observed. A generalized linear model revealed that the extent to which a template can be improved can be predicted using four variables. Templates with the greatest scope for improvement tend to have relatively more fragments, shorter fragments, higher precentage of helical secondary structure, and lower sequence identity. Optimal positioning of the template fragments offers the potential for improving loop modelling. These results demonstrate that substantial improvement could be made on many templates if the conserved fragments were to be optimally positioned. They also provide a basis for identifying templates for which modification of fragment positions may yield such improvements. Contact:
Structural bioinformatics Advance Access publication June 4, 2010 Exploring the potential of template-based modelling
, 2010
"... Motivation: Template-based modelling can approximate the unknown structure of a target protein using an homologous template structure. The core of the resulting prediction then comprises the structural regions conserved between template and target. Target prediction could be improved by rigidly repo ..."
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Motivation: Template-based modelling can approximate the unknown structure of a target protein using an homologous template structure. The core of the resulting prediction then comprises the structural regions conserved between template and target. Target prediction could be improved by rigidly repositioning such single template, structurally conserved fragment regions. The purpose of this article is to quantify the extent to which such improvements are possible and to relate this extent to properties of the target, the template and their alignment. Results: The improvement in accuracy achievable when rigid fragments from a single template are optimally positioned was calculated using structure pairs from the HOMSTRAD database, as well as CASP7 and CASP8 target/best template pairs. Over the union of the structurally conserved regions, improvements of 0.7Å in root mean squared deviation (RMSD) and 6 % in GDT_HA were commonly observed. A generalized linear model revealed that the extent to which a template can be improved can be predicted using four variables. Templates with the greatest scope for improvement tend to have relatively more fragments, shorter fragments, higher percentage of helical secondary structure and lower sequence identity. Optimal positioning of the template fragments offers the potential for improving loop modelling. These results demonstrate that substantial improvement could be made on many templates if the conserved fragments were to be optimally positioned. They also provide a basis for identifying templates for which modification of fragment positions may yield such improvements.
PROTEINS: Structure, Function, and Genetics 5139-148 (1989) Structural Principles of a/p Barrel Proteins: The Packing of the Interior of the Sheet
"... ABSTRACT alp barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded P-sheets and the packing of the residues at the cent ..."
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ABSTRACT alp barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded P-sheets and the packing of the residues at the center of the barrel. The packing in this region is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO and TIM can be understood in terms of distortions of this simple pattern, caused by residues with small side chains at some of the positions inside the barrel. Two classes of packing are found. In one class, to which RubisCO and TIM belong, the central layer is formed by a residue from the first, third, fifth, and seventh strands; the upper and lower layers are formed by residues from the second, fourth, sixth, and eighth strands. In the second class, to which GAO belongs, this is reversed: it is side chains from the even-numbered strands that form the central layer, and side chains from the oddnumbered strands that form the outer layers. Our results suggest that not all proteins with this fold are related by evolution, but that they represent a common favorable solution to the structural problems involved in the creation of a closed Q barrel. Key words: protein architecture, packing, evolutionary relationships
STANDARD REFERENCE MATERIALS 5 Standard Reference Materials 3191-3195-Aqueous Electrolytic Conductance Standards
, 1990
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