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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
Published on: October 15, 2018
Cálculos conjuntos de proteínas no estructuradas restringidas por datos RDC y PRE: un estudio de caso de la
Jie-rong Huang1, Stephan Grzesiek
1Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
Journal of the American Chemical Society
|December 17, 2009
Resumen
Caracterizar las proteínas desplegadas es un desafío. Los nuevos métodos computacionales que utilizan el acoplamiento dipolar residual (RDC) y los datos de mejora de la relajación paramagnética (PRE) permiten un análisis detallado de los conjuntos conformacionales de proteínas.
Área de la Ciencia:
- La biofísica es la biofísica.
- Biología Estructural Biología estructural.
- Biología computacional Biología computacional.
Sus antecedentes:
- La caracterización de los estados de proteínas desplegadas es difícil debido a sus complejos conjuntos conformacionales.
- El acoplamiento dipolar residual (RDC) y la mejora de la relajación paramagnética (PRE) proporcionan datos experimentales sobre estos estados.
Objetivo del estudio:
- Desarrollar nuevos módulos computacionales para analizar los estados de proteínas desplegadas utilizando datos de RDC y PRE.
- Para crear un modelo mínimo de conjuntos de proteínas desplegadas.
Principales métodos:
- Desarrolló nuevos módulos para XPLOR-NIH para incorporar RDC y PREs de alineación estérica como restricciones.
- Se realizaron cálculos de conjunto sobre la ubiquitina desnaturalizada con urea utilizando 419 RDC y 253 PREs.
- Los contactos y las poblaciones conformacionales C ((alfa) analizados.
Principales resultados:
- Un pequeño número de conformadores (alrededor de 10) es suficiente para reproducir los datos experimentales de RDC, PRE y radio de giro.
- Se observaron poblaciones significativas (10-20%) de conformaciones similares al estado A en el conjunto desplegado.
- Se obtuvieron resultados similares utilizando solo RDCs o PREs, y ambos métodos permitieron la detección de subconformaciones de baja población.
Conclusiones:
- Los métodos computacionales desarrollados basados en RDC y PRE permiten la detección estadísticamente significativa de subconformaciones en conjuntos de proteínas desplegadas.
- La desnaturalización de urea y metanol/ácido conduce a estados similares de baja energía en conjuntos de proteínas.
- Estos métodos ofrecen un enfoque poderoso para caracterizar cuantitativamente los intermediarios de plegamiento de proteínas y los estados desplegados.
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