Understanding disordered and membrane protein recognition by molecular dynamics

Stanley, Nathaniel H.

Understanding disordered and membrane protein recognition by molecular dynamics

Document Type

Doctoral thesis
Published Version

Author

Stanley, Nathaniel H.

Director

De Fabritiis, Gianni

Publication Date

2015-04-24

Pages

123 p.

Citation

Stanley, N. Understanding disordered and membrane protein recognition by molecular dynamics. Universitat Pompeu Fabra; 2015. handle: http://hdl.handle.net/10803/384535

This citation was generated automatically.

Doctoral program

Programa de doctorat en Biomedicina

Abstract

This thesis has been about the use of a simulation technique, known as molecular dynamics simulations, to study biophysics in proteins that have historically been difficult to study with other methods. We have studied numerous systems, namely binding to the membrane proteins Fatty acid amide hydrolase (FAAH) and the sphingosine-1-phosphate receptor 1 (S1P1R), and folding in the disordered protein kinase inducible domain (KID). In each case we have been able to analyze processes and uncover behaviors that are difficult or impossible to view by other means.
Esta tesis se trata del uso de un técnica de simulación, llamado simulación de dinámica molecular, para estudiar la biofísica de proteínas que históricamente han estado difícil estudiar por otros métodos. Hemos estudiado numerosas sistemas, en particular la encuadernación de ligandos en sistemas de membranas como Fatty acid amide hydrolase (FAAH) y el receptor Sphingosine-1-phosphate (S1P1R), y cómo se pliegue una proteína desordenada llamado Kinase inducible domain (KID). En cada caso hemos sido capaz de analizar procesos y detapar comportamientos que sean difícil o imposible ver por otros métodos.

Keywords

Molecular dynamics, Intrinsically disordered proteins, Membrane proteins, Markov state models, Dinàmica molecular, Models d'estat de Markov, Proteïnes desordenades, Proteïnes de membranes