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Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods
Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA
Department of Computer Science, State University of New York Korea, Incheon 406-840, Korea
* Author to whom correspondence should be addressed.
Received: 30 July 2013; in revised form: 17 September 2013 / Accepted: 19 September 2013 / Published: 15 October 2013
Abstract: With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.
Keywords: constraint-base structure prediction; integrative structure prediction; sequence variants; protein dynamics; mass spectrometry
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MDPI and ACS Style
Pi, J.; Sael, L. Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods. Int. J. Mol. Sci. 2013, 14, 20635-20657.
Pi J, Sael L. Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods. International Journal of Molecular Sciences. 2013; 14(10):20635-20657.
Pi, Jaewoo; Sael, Lee. 2013. "Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods." Int. J. Mol. Sci. 14, no. 10: 20635-20657.