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Biotin Complex (biotin + complex)
Selected AbstractsFully quantum mechanical energy optimization for protein,ligand structureJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2004Yun Xiang Abstract We present a quantum mechanical approach to study protein,ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein,ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein,ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree,Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein,ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin,biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein,ligand interaction. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1431,1437, 2004 [source] Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetasePROTEIN SCIENCE, Issue 3 2002Keehwan Kwon Abstract The binding of the Escherichia coli biotin holoenzyme synthetase to the two ligands, biotin and bio-5,-AMP, is coupled to disorder-to-order transitions in the protein. In the structure of the biotin complex, a "glycine-rich" loop that is disordered in the apo-enzyme is folded over the ligand. Mutations in three residues in this loop result in significant changes in the affinity of the enzyme for both biotin and bio-5,-AMP. The kinetic basis of these losses in the affinity resides primarily in changes in the unimolecular rates of dissociation of the complexes. In this work, isothermal titration calorimetry has been employed to examine the detailed thermodynamics of binding of three loop mutants to biotin and bio-5,-AMP. The energetic features of dissociation of the protein,ligand complexes also have been probed by measuring the temperature dependencies of the unimolecular dissociation rates. Analysis of the data using the Eyring formalism yielded entropic and enthalpic contributions to the energetic barrier to dissociation. The thermodynamic results coupled with the known structures of the apo-enzyme and biotin complex have been used to formulate a model for progression from the ground-state complex to the transition state in biotin dissociation. In this model, the transition-state is characterized by both partial disruption of noncovalent bonds and acquisition of some of the disorder that characterizes the glycine-rich loop in the absence of ligand. [source] Challenging semi-bootstrapping molecular-replacement strategy reveals intriguing crystal packing of rhizavidinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Amit Meir The structure of rhizavidin, the first dimeric member of the avidin family which maintains high affinity towards biotin, was determined to high resolution by SeMet SAD. Consequently, the structure of the rhizavidin,biotin complex was determined by molecular-replacement methods using the apo structure as the search model; this ran into complications and required combined programs as well as bootstrapping approaches. Although present as a dimer in solution, rhizavidin packs as unique oligomers in both crystal forms. The novel insights derived from the unique molecular-replacement procedure and the crystal-driven oligomeric forms in this work may have utililty in biotechological and nanotechnological applications. [source] UV resonance Raman study of streptavidin binding of biotin and 2-iminobiotin: Comparison with avidinBIOPOLYMERS, Issue 6 2001John Clarkson Abstract UV resonance Raman (UVRR) spectroscopy is used to study the binding of biotin and 2-iminobiotin by streptavidin, and the results are compared to those previously obtained from the avidin,biotin complex and new data from the avidin,2-iminobiotin complex. UVRR difference spectroscopy using 244-nm excitation reveals changes to the tyrosine (Tyr) and tryptophan (Trp) residues of both proteins upon complex formation. Avidin has four Trp and only one Tyr residue, while streptavidin has eight Trp and six Tyr residues. The spectral changes observed in streptavidin upon the addition of biotin are similar to those observed for avidin. However, the intensity enhancements observed for the streptavidin Trp Raman bands are less than those observed with avidin. The changes observed in the streptavidin Tyr bands are similar to those observed for avidin and are assigned exclusively to the binding site Tyr 43 residue. The Trp and Tyr band changes are due to the exclusion of water and addition of biotin, resulting in a more hydrophobic environment for the binding site residues. The addition of 2-iminobiotin results in spectral changes to both the streptavidin and avidin Trp bands that are very similar to those observed upon the addition of biotin in each protein. The changes to the Tyr bands are very different than those observed with the addition of biotin, and similar spectral changes are observed in both streptavidin and avidin. This is attributable to hydrogen bond changes to the binding site Tyr residue in each protein, and the similar Tyr difference features in both proteins supports the exclusive assignment of the streptavidin Tyr difference features to the binding site Tyr 43. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 307,314, 2001 [source] | ||||||||||