Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis

Proteins synthesized in the cell can begin to fold during translation, before the entire polypeptide has been produced. Previously, we investigated the cotranslational folding of three different repeats of a-spectrin by Force Profile Analysis (FPA), and compared the results to in vitro folding data obtained with purified proteins. We observed that cotranslational folding of the 16 th a-spectrin repeat (the R16 domain) commenced at a shorter nascent chain length when it was preceded by the R15 domain compared to when being produced alone. Here, we extend this result to study how the cotranslational folding behavior of the R15 and R16 domains are affected by their neighboring R14 and R17 domains. Our results show that the domains impact each other's folding in distinct ways, that may be important for the efficient assembly of a-spectrin. We further estimate that the R16 domain can exert a force on the nascent chain of ~15 pN during cotranslational folding.

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“…can generate a maximal force of 15-20 pN on the AP, Fig. 4, in line with theoretical estimates based on MD simulations 46,47 .…”

Section: Discussionsupporting

confidence: 88%

Cotranslational folding cooperativity of contiguous domains of α-spectrin

Kemp

Nilsson

Tian

et al. 2019

Preprint

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“…The linker lengths used in these simulations were chosen such that they bracketed the length at which the midpoint of folding occurred. It was recently found that the unfolded state of a nascent chain can generate an entropic pulling force on the ribosome 7 , and attractive interactions between the nascent chain and outer ribosome surface also have the potential to give rise to forces 22 . To isolate the force arising from domain folding we ran additional simulations in which the domains always remain unfolded (see SI Appendix) and simulated these folding-incompetent proteins on arrested ribosomes at the same linker lengths.…”

Section: Resultsmentioning

confidence: 99%

“…Tensile forces acting on the nascent protein can alter the speed of translation elongation in a form of mechanical allosteric communication that links what happens outside the exit tunnel to the ribosome's catalytic core [1][2][3][4][5][6][7] . It has been found that protein folding on translationally arrested ribosomes can generate a pulling force that is transmitted through the nascent protein backbone to the peptidyl transferase center (PTC), which can alter peptide bond formation 1,4,7 . Specifically, a previous study used Quantum Mechanics/Molecular Mechanics simulations to show that pulling forces applied to the PTC can decrease the free energy of the transition state barrier to peptide bond formation 7 .…”

Section: Discussionmentioning

confidence: 99%

“…Mechanical forces acting on a nascent polypeptide chain can alter the speed of protein synthesis by the ribosome [1][2][3][4][5][6][7] . Such changes in translation speed can influence the timing and efficiency of a variety of co-translational processes affecting the fold 8,9 , function 10,11 , and intracellular localization of the newly synthesized protein 12,13 .…”

mentioning

confidence: 99%

“…1a,b). That pulling force is transmitted 10 nm back to the catalytic core of the ribosome in a form of mechanical allosteric communication, altering the energy barrier to peptide bond formation 7 , thereby influencing translation speed. The factors governing co-translational force generation have not yet been identified, but they are important to understand as they can modulate translation speed which can alter protein structure and affect the evolutionary selection pressures shaping the sequence and properties of both mRNA and proteins.…”

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confidence: 99%

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Domain topology, stability, and translation speed determine mechanical force generation on the ribosome

Leininger

Trovato

Nissley

et al. 2018

Preprint

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The concomitant folding of a nascent protein domain with its synthesis can generate mechanical forces that act on the ribosome and alter translation speed. Such changes in speed can affect the structure and function of the newly synthesized protein as well as cellular phenotype. The domain properties that govern force generation have yet to be identified and understood, and the influence of translation speed is unknown as all reported measurements have been carried out on arrested ribosomes. Here, using coarse-grained molecular simulations and statistical mechanical modeling of protein synthesis, we demonstrate that force generation is determined by a domain's stability and topology, as well as translation speed. The statistical mechanical models we create predict how force profiles depend on these properties. These results indicate that force measurements on arrested ribosomes will not always accurately reflect what happens in a cell, especially for slow-folding domains, and suggest the possibility that certain domain properties may be enriched or depleted across the structural proteome of organisms through evolutionary selection pressures to modulate protein synthesis speed and post-translational protein behavior.Page 2 of 30 Significance StatementMechanochemistry, the influence of molecular-scale mechanical forces on chemical processes, can occur on actively translating ribosomes through the force-generating actions of motor proteins and the co-translational folding of domains. Such forces are transmitted to the ribosome's catalytic core and alter rates of protein synthesis; representing a form of mechanical allosteric communication. These changes in translation-elongation kinetics are biologically important because they can influence protein structure, function, and localization within a cell. Many fundamental questions are unresolved concerning the properties of protein domains that determine mechanical force generation, the effect of translation speed on this force, and exactly how, at the molecular level, force is generated. In this study we answer these questions using cutting-edge molecular simulations and statistical mechanical modeling.

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Co‐translational folding of nascent polypeptides: Multi‐layered mechanisms for the efficient biogenesis of functional proteins

et al. 2021

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The coupling of protein synthesis and folding is a crucial yet poorly understood aspect of cellular protein folding. Over the past few years, it has become possible to experimentally follow and define protein folding on the ribosome, revealing principles that shape co‐translational folding and distinguish it from refolding in solution. Here, we highlight some of these recent findings from biochemical and biophysical studies and their potential significance for cellular protein biogenesis. In particular, we focus on nascent chain interactions with the ribosome, interactions within the nascent protein, modulation of translation elongation rates, and the role of mechanical force that accompanies nascent protein folding. The ability to obtain mechanistic insight in molecular detail has set the stage for exploring the intricate process of nascent protein folding. We believe that the aspects discussed here will be generally important for understanding how protein synthesis and folding are coupled and regulated.

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Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis

Cited by 38 publications

References 75 publications

Cotranslational folding cooperativity of contiguous domains of α-spectrin

Cotranslational folding cooperativity of contiguous domains of α-spectrin

Domain topology, stability, and translation speed determine mechanical force generation on the ribosome

Co‐translational folding of nascent polypeptides: Multi‐layered mechanisms for the efficient biogenesis of functional proteins

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