Handle URI:
http://hdl.handle.net/10754/597315
Title:
A Motion Planning Approach to Studying Molecular Motions
Authors:
Amato, Nancy M.; Tapia, Lydia; Thomas, Shawna
Abstract:
While structurally very different, protein and RNA molecules share an important attribute. The motions they undergo are strongly related to the function they perform. For example, many diseases such as Mad Cow disease or Alzheimer's disease are associated with protein misfolding and aggregation. Similarly, RNA folding velocity may regulate the plasmid copy number, and RNA folding kinetics can regulate gene expression at the translational level. Knowledge of the stability, folding, kinetics and detailed mechanics of the folding process may help provide insight into how proteins and RNAs fold. In this paper, we present an overview of our work with a computational method we have adapted from robotic motion planning to study molecular motions. We have validated against experimental data and have demonstrated that our method can capture biological results such as stochastic folding pathways, population kinetics of various conformations, and relative folding rates. Thus, our method provides both a detailed view (e.g., individual pathways) and a global view (e.g., population kinetics, relative folding rates, and reaction coordinates) of energy landscapes of both proteins and RNAs. We have validated these techniques by showing that we observe the same relative folding rates as shown in experiments for structurally similar protein molecules that exhibit different folding behaviors. Our analysis has also been able to predict the same relative gene expression rate for wild-type MS2 phage RNA and three of its mutants.
Citation:
Amato NM, Tapia L, Thomas S (2010) A Motion Planning Approach to Studying Molecular Motions. Communications in Information and Systems 10: 53–68. Available: http://dx.doi.org/10.4310/cis.2010.v10.n1.a4.
Publisher:
International Press of Boston
Journal:
Communications in Information and Systems
KAUST Grant Number:
KUS-C1-016-04
Issue Date:
2010
DOI:
10.4310/cis.2010.v10.n1.a4
Type:
Article
ISSN:
1526-7555; 2163-4548
Sponsors:
This research supported in part by NSF Grants EIA-01037-42, ACR-0081510, ACR-0113971, CCR-0113974, ACI-0326350, CRI-0551685, CCF-0833199, CCF-830753, by Chevron, IBM, Intel, HP, and by King Abdullah University of Science and Technology (KAUST) Award KUS-C1-016-04. Tapia supported in part by a Sloan scholarship, PEO scholarship, NIH Molecular Biophysics Training Grant (T32GM065088) and a Department of Education (GAANN) Fellowship. Thomas supported in part by an NSF Graduate Research Fellowship, a PEO scholarship, a
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Full metadata record

DC FieldValue Language
dc.contributor.authorAmato, Nancy M.en
dc.contributor.authorTapia, Lydiaen
dc.contributor.authorThomas, Shawnaen
dc.date.accessioned2016-02-25T12:30:31Zen
dc.date.available2016-02-25T12:30:31Zen
dc.date.issued2010en
dc.identifier.citationAmato NM, Tapia L, Thomas S (2010) A Motion Planning Approach to Studying Molecular Motions. Communications in Information and Systems 10: 53–68. Available: http://dx.doi.org/10.4310/cis.2010.v10.n1.a4.en
dc.identifier.issn1526-7555en
dc.identifier.issn2163-4548en
dc.identifier.doi10.4310/cis.2010.v10.n1.a4en
dc.identifier.urihttp://hdl.handle.net/10754/597315en
dc.description.abstractWhile structurally very different, protein and RNA molecules share an important attribute. The motions they undergo are strongly related to the function they perform. For example, many diseases such as Mad Cow disease or Alzheimer's disease are associated with protein misfolding and aggregation. Similarly, RNA folding velocity may regulate the plasmid copy number, and RNA folding kinetics can regulate gene expression at the translational level. Knowledge of the stability, folding, kinetics and detailed mechanics of the folding process may help provide insight into how proteins and RNAs fold. In this paper, we present an overview of our work with a computational method we have adapted from robotic motion planning to study molecular motions. We have validated against experimental data and have demonstrated that our method can capture biological results such as stochastic folding pathways, population kinetics of various conformations, and relative folding rates. Thus, our method provides both a detailed view (e.g., individual pathways) and a global view (e.g., population kinetics, relative folding rates, and reaction coordinates) of energy landscapes of both proteins and RNAs. We have validated these techniques by showing that we observe the same relative folding rates as shown in experiments for structurally similar protein molecules that exhibit different folding behaviors. Our analysis has also been able to predict the same relative gene expression rate for wild-type MS2 phage RNA and three of its mutants.en
dc.description.sponsorshipThis research supported in part by NSF Grants EIA-01037-42, ACR-0081510, ACR-0113971, CCR-0113974, ACI-0326350, CRI-0551685, CCF-0833199, CCF-830753, by Chevron, IBM, Intel, HP, and by King Abdullah University of Science and Technology (KAUST) Award KUS-C1-016-04. Tapia supported in part by a Sloan scholarship, PEO scholarship, NIH Molecular Biophysics Training Grant (T32GM065088) and a Department of Education (GAANN) Fellowship. Thomas supported in part by an NSF Graduate Research Fellowship, a PEO scholarship, aen
dc.publisherInternational Press of Bostonen
dc.titleA Motion Planning Approach to Studying Molecular Motionsen
dc.typeArticleen
dc.identifier.journalCommunications in Information and Systemsen
dc.contributor.institutionParasol Lab, Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77845en
kaust.grant.numberKUS-C1-016-04en
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