An important current goal in molecular biology is to understand how the synthesis and folding of proteins are coupled to each other. Although the understanding of events that occur as a protein is synthesized by the ribosome has been aided by high-resolution structures of many of the macromolecular components, only low-resolution views of the structure and dynamics of ribosome nascent-chain complexes (RNCs) are currently available. More importantly, essentially all studies of RNCs have been performed under conditions in which the RNC is stalled, i.e. under conditions in which its conformational dynamics are effectively at thermodynamic equilibrium. There is increasing evidence, however, that the fates of nascent proteins can depend significantly on the rate at which translation occurs, which implies that the partitioning of a newly synthesized protein between misfolded and native conformations is at least partly under kinetic control. There is, therefore, an urgent need for methods that can structurally characterize RNCs during active translation. Since experimental characterization is likely to remain an intractable problem it is proposed here to use molecular simulation methods instead. A plan of work is therefore outlined for developing a simulation framework that can accurately model coupled synthesis-folding events in the bacterial ribosome and that can fully define the role of its attached chaperone, trigger factor (TF), both in isolated monosomes and in models of complete polysomes.
Three Specific Aims will be pursued. First, explicit-solvent molecular dynamics simulations will be used to determine the extent of trigger factor's conformational flexibility alone and in complex with the ribosome. These studies will establish the limits of TF's conformational adaptability in its functionally relevant states and will provide the basis for developing a realistic simulation model of TF-RNCs. Second, an accurate coarse-grained (CG) simulation model will be developed that allows the conformational behavior of stalled TF-RNC complexes to be directly modeled;properly parameterized, this model will enable a wide range of experimental observations on TF-RNCs to be rationalized at a truly structural level. Finally, the CG simulation model will be used to simulate cotranslational folding events in actively translating RNC complexes (with and without TF) in monosomes and polysomes. These latter studies will provide structural and dynamic pictures of nascent protein chains from the moment that they emerge from the ribosome's exit tunnel to the moment that they complete folding or misfolding in a way that is not achievable by conventional experimental methods. As such, the proposed studies are expected to greatly improve understanding of the factors that affect a nascent protein's propensity to fold or misfold during the course of its translation.

Public Health Relevance

The proposed work is relevant to public health because it seeks to understand one of the potential origins of intracellular protein misfolding, an event now known to be implicated in a number of diseases. The work is relevant to the NIGMS's mission because it seeks to understand the basic science underpinning the cotranslational folding of proteins as they are synthesized by the ribosome, accounting also for the role(s) played by chaperones and assembly into polysomes.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM099865-02
Application #
8412763
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Wehrle, Janna P
Project Start
2012-01-15
Project End
2015-12-31
Budget Start
2013-01-01
Budget End
2013-12-31
Support Year
2
Fiscal Year
2013
Total Cost
$243,871
Indirect Cost
$55,696
Name
University of Iowa
Department
Biochemistry
Type
Schools of Medicine
DUNS #
062761671
City
Iowa City
State
IA
Country
United States
Zip Code
52242
Natan, Eviatar; Endoh, Tamaki; Haim-Vilmovsky, Liora et al. (2018) Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nat Struct Mol Biol 25:279-288
Miller, Mark S; Lay, Wesley K; Li, Shuxiang et al. (2017) Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations. J Chem Theory Comput 13:1812-1826
Andrews, Casey T; Campbell, Brady A; Elcock, Adrian H (2017) Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 13:1794-1811
Lay, Wesley K; Miller, Mark S; Elcock, Adrian H (2016) Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. J Chem Theory Comput 12:1401-7
Miller, Mark S; Lay, Wesley K; Elcock, Adrian H (2016) Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization. J Phys Chem B 120:8217-29
Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang et al. (2015) Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. J Chem Theory Comput 11:2341-54
Schrodt, Michael V; Andrews, Casey T; Elcock, Adrian H (2015) Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 ?s Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 11:5906-17
Brown, Reid F; Andrews, Casey T; Elcock, Adrian H (2015) Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment. J Chem Theory Comput 11:2315-28
Li, Shuxiang; Elcock, Adrian H (2015) Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins. J Phys Chem Lett 6:2127-33
Li, Shuxiang; Andrews, Casey T; Frembgen-Kesner, Tamara et al. (2015) Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. J Chem Theory Comput 11:1315-29

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