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1.
J Biomol NMR ; 30(1): 71-80, 2004 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-15452436

RESUMO

We present QSim, a program for simulation of NMR experiments. Pulse sequences are implemented and analyzed in QSim using a mouse driven interface. QSim can handle almost any modern NMR experiment, using multiple channels, shaped pulses, mixing, decoupling, phase-cycling and pulsed field gradients. Any number of spins with any spin quantum number can, in theory, be used in simulations. Relaxation is accounted for during all steps of pulse sequences and relaxation interference effects are supported. Chemical kinetics between any numbers of states can be simulated. Both classical and quantum mechanical calculations can be performed. The result of a simulation can be presented either as magnetization as a function of time or as a processed spectrum.


Assuntos
Simulação por Computador , Ressonância Magnética Nuclear Biomolecular , Gráficos por Computador , Cinética , Computação Matemática , Matemática , Isótopos de Nitrogênio , Prótons , Teoria Quântica , Marcadores de Spin , Temperatura , Fatores de Tempo
2.
Proc Natl Acad Sci U S A ; 100(6): 3185-90, 2003 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-12594333

RESUMO

Combinatorial protein engineering provides powerful means for functional selection of novel binding proteins. One class of engineered binding proteins, denoted affibodies, is based on the three-helix scaffold of the Z domain derived from staphylococcal protein A. The Z(SPA-1) affibody has been selected from a phage-displayed library as a binder to protein A. Z(SPA-1) also binds with micromolar affinity to its own ancestor, the Z domain. We have characterized the Z(SPA-1) affibody in its uncomplexed state and determined the solution structure of a Z:Z(SPA-1) protein-protein complex. Uncomplexed Z(SPA-1) behaves as an aggregation-prone molten globule, but folding occurs on binding, and the original (Z) three-helix bundle scaffold is fully formed in the complex. The structural basis for selection and strong binding is a large interaction interface with tight steric and polar/nonpolar complementarity that directly involves 10 of 13 mutated amino acid residues on Z(SPA-1). We also note similarities in how the surface of the Z domain responds by induced fit to binding of Z(SPA-1) and Ig Fc, respectively, suggesting that the Z(SPA-1) affibody is capable of mimicking the morphology of the natural binding partner for the Z domain.


Assuntos
Anticorpos/química , Proteínas de Transporte/química , Anticorpos/genética , Anticorpos/metabolismo , Sítios de Ligação , Proteínas de Transporte/genética , Proteínas de Transporte/metabolismo , Cristalografia por Raios X , Técnicas In Vitro , Substâncias Macromoleculares , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Biblioteca de Peptídeos , Engenharia de Proteínas , Dobramento de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteína Estafilocócica A/química , Proteína Estafilocócica A/genética , Proteína Estafilocócica A/metabolismo
3.
Biophys J ; 83(5): 2812-25, 2002 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-12414713

RESUMO

Tyrosine ring dynamics of the gastrointestinal hormone motilin was studied using two independent physical methods: fluorescence polarization anisotropy decay and NMR relaxation. Motilin, a 22-residue peptide, was selectively (13)C labeled in the ring epsilon-carbons of the single tyrosine residue. To eliminate effects of differences in peptide concentration, the same motilin sample was used in both experiments. NMR relaxation rates of the tyrosine ring C(epsilon)-H(epsilon) vectors, measured at four magnetic field strengths (9.4, 11.7, 14.1, and 18.8 Tesla) were used to map the spectral density function. When the data were analyzed using dynamic models with the same number of components, the dynamic parameters from NMR and fluorescence are in excellent agreement. However, the estimated rotational correlation times depend on the choice of dynamic model. The correlation times estimated from the two-component model-free approach and the three-component models were significantly different (1.7 ns and 2.2 ns, respectively). Various earlier studies of protein dynamics by NMR and fluorescence were compared. The rotational correlation times estimated by NMR for samples with high protein concentration were on average 18% longer for folded monomeric proteins than the corresponding times estimated by fluorescence polarization anisotropy decay, after correction for differences in viscosity due to temperature and D(2)O/H(2)O ratio.


Assuntos
Anisotropia , Motilina/química , Tirosina/química , Animais , Fenômenos Biofísicos , Biofísica , Espectroscopia de Ressonância Magnética/métodos , Modelos Teóricos , Peptídeos/química , Prótons , Espectrometria de Fluorescência/métodos , Temperatura , Fatores de Tempo
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