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Structure-based predictive models for allosteric hot spots.
(2009) PLoS Comput Biol 5
PubMed: 19816556 | PubMedCentral: PMC2748687 | DOI: 10.1371/journal.pcbi.1000531
PDB of effector ligand-unbound (inactive state) PDB of effector ligand-bound (active state) Training Data Set Proteins CheY (signal transduction) 3chy 1fqw PurR repressor (transcription factor) 1dbq 1... et Tet repressor (transcription factor) 2trt 1qpi Hemoglobin (carrier protein/enzyme) 4hhb 1hho Phosphofructokinase (enzyme) 6pfk 4pfk phosphoglycerate dehydrogenase (enzyme) 1psd 1yba fructose-1,6-bisphosphatase (enzyme) 1eyj 1eyi Aspartate transcarbamoylase (enzyme) 1rac 1d09 RhoA (signal transduction) 1ftn 1a2b CDC-42 (signal transduction) 1an0 1nf3 glycogen phosphorylase (transcription factor) 1gpb 7gpb Independent Data Set Proteins glucokinase (enzyme) 1v4t 1v4s glutamate dehydrogenase (enzyme) 1nr7 1hwz lac repressor (transcription factor) 1tlf 1efa myosin II (motor protein/enzyme) 1vom 1fmw thrombin (enzyme) 1sgi 1sg8 Since the Michaelis constant, K M , has been shown to be an apparent dissociation constant, taking into account all substrate-bound species of enzyme, and is directly proportional to K S , we may replace K S with K M in (2)  .
Publication Year: 2009
Fast optimization of statistical potentials for structurally constrained phylogenetic models.
(2009) BMC Evol Biol 9
PubMed: 19740424 | PubMedCentral: PMC2754480 | DOI: 10.1186/1471-2148-9-227
G LOBIN 15-144 is made of 15 vertebrates sequences of the β -globin gene (taken from the original dataset from [ 36 ]), with a protein structure defined by the PDB file 4HHB and a tree topolog... estimated using Phylobayes 3.1c [ 37 ] (which is consistent with the tree topology described in [ 38 ]).
The RCSB Protein Data Bank: redesigned web site and web services.
(2011) Nucleic Acids Res 39
PubMed: 21036868 | PubMedCentral: PMC3013649 | DOI: 10.1093/nar/gkq1021
RESTful services are easy to use; for example the following URL: http://www.pdb.org/pdb/rest/describeMol?structureId=4hhb specifies a fetch service that returns a description in XML format for the pol... mer entities in PDB entry 4HHB: <structureId id="4HHB"> <polymerDescriptions> <polymer entityNr="1" length="141" type="polypeptide(L)"> <chain id="A"/> <chain id="C"/> <polymerDescription description="HEMOGLOBIN (DEOXY) (ALPHA CHAIN)"/> </polymer> <polymer entityNr="2" length="146" type="polypeptide(L)"> <chain id="B"/> <chain id="D"/> <polymerDescription description="HEMOGLOBIN (DEOXY) (BETA CHAIN)"/ > </polymer> </polymerDescriptions> </structureId> This information can be easily parsed with an XML parser and used by an application or web site.
Publication Year: 2011
In silico analysis of single nucleotide polymorphism (SNPs) in human ?-globin gene.
(2011) PLoS One 6
PubMed: 22028795 | PubMedCentral: PMC3197589 | DOI: 10.1371/journal.pone.0025876
The available protein structure of HBB gene showed PDB ID: 4HHB and HBB mutations showing β-Hemoglobinopathies on the ß-chain were following (1) HbC β 6; AA Glu→Lys (E&... x02192;K), (2) HbD β 121; AA Glu→Gln (E→Q), (3) HbE β 26; Glu→Lys (E→K), and (4) HbS β 6; Glu→Val (E→V).
nsSNPs location modeling on protein structure The single amino acid polymorphism database (SAAP)  and dbSNPs were used to recognize the protein encoded by HBB gene (PDB ID: 4HHB) and identified single point mutation residue positions.
The energy calculations of mutation residues were done only on β2 chains of HBB gene (PDB ID: 4HHB).
However, in the present study we used a different protein (PDB ID: 4HHB) of HBB gene based on the clinical report of a patient (#0051421) from the test directory of ARUP laboratory, USA.
The energy minimizations studies of the native type protein (4HHB) and the mutant type structures showed that the total energy of the native type protein structure after energy minimization was −334380.5 kJ/mol (score; 0.69), which was 29644578.1 kJ/mol (score: −3.31) prior to energy minimization.
The energy minimizations studies were done by NOMAD-Ref server for the native type protein (4HHB) and the mutant type structures, the total energy for the native type protein structure (4HHB) following energy minimization was −334380.5 kJ/mol (score; 0.69), where as prior to energy minimization it was 29644578.1 kJ/mol (score: −3.31).
The energy minimizations were achieved by YASARA and NOMAD-Ref Gromacs server using force field energy for the native type protein 4HHB and mutant type protein structures from the protein model RMSD.
t003 Table 3 RMSD and total energy of native structure (4HHB) and mutant modeled structures.
The total energy of native structure 4HHB and mutant model structure residues were calculated ( Table 3 ) and showed range from 0.25 to 0.50 RMSD native and mutant protein structure, respectively.
Hemoglobin interactions with ?B crystallin: a direct test of sensitivity to protein instability.
(2012) PLoS One 7
PubMed: 22815750 | PubMedCentral: PMC3399823 | DOI: 10.1371/journal.pone.0040486
Data sets for the high resolution X-ray diffraction structures of human deoxy-hemoglobinA (PDB:4HHB) and deoxy-hemoglobin S (PDB:2HBS) were obtained from the Protein Data Bank ( www.PDB.org ).
Top Left: The molecular structure of normal Hemoglobin A (PDB:4HHB).
Publication Year: 2012
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