The Ribosome Modulates Nascent Protein Folding

Kaiser, Christian; Goldman, Daniel; Chodera, John D.; Tinoco, Ignacio; Bustamante, Carlos

doi:10.1126/science.1209740

Cited by 274 publications

(377 citation statements)

References 62 publications

Supporting

Mentioning

354

Contrasting

Order By: Relevance

“…It is interesting to note that the presence of the exit tunnel leads to an increase of about 4% in P f old at large t. Thus, the exit tunnel has a favorable effect on folding efficiency. This finding is consistent with recent experimental result [12] on the folding of T4 lysozyme with and without the ribosome. The successful folding probability, P f old , of 1PGA protein in three cases: a) refolding (without translation), b) cotranslational folding without the exit tunnel and c) cotranslational folding with exit tunnel.…”

Section: Effect Of Ribosomal Exit Tunnel On the Successful Folding Prsupporting

confidence: 94%

See 1 more Smart Citation

Effects of ribosomal exit tunnel on protein's cotranslational folding

Bui¹,

Hoang²

2013

Comm. in Phys.

View full text Add to dashboard Cite

Abstract. In vivo, folding of many proteins occurs during their synthesis in the ribosome and continues after they have escaped from the ribosomal exit tunnel. In this research, we investigate the confinement effects of the ribosome on the cotranslational folding of three proteins, of PDB codes 1PGA, 1CRN and 2RJX, by using a coarse-grained model and molecular dynamics simulation. The exit tunnel is modeled as a hollow cylinder attached to a flat wall, whereas a Go

show abstract

Section: Effect Of Ribosomal Exit Tunnel On the Successful Folding Prsupporting

confidence: 94%

“…nascent polypeptide chain starts to fold during their synthesis in the ribosome [9][10][11]. Furthermore, the ribosome has been shown to promote efficient folding of nascent proteins [12]. Interestingly, the non-equilibrium character of the translational process also favors the formation of helices near the C-terminus [13].…”

Section: Introductionmentioning

confidence: 99%

Effects of ribosomal exit tunnel on protein's cotranslational folding

Bui¹,

Hoang²

2013

Comm. in Phys.

View full text Add to dashboard Cite

show abstract

“…The secondary structures of 2EFV consists of four helices (23-32, 41-49, 62-71, 74-86), two 3-10 helices (33-35, 72-73), and two β -strands (12)(13)(14)(15)(16)(17)(54)(55)(56)(57)(58)(59). The knot is of the trefoil type and its ends are located at sites 11 and 73.…”

Section: A 2efvmentioning

confidence: 99%

Structural entanglements in protein complexes

Zhao

Chwastyk

Cieplak

2017

The Journal of Chemical Physics

View full text Add to dashboard Cite

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface, and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.

show abstract

“…With many improvements, the Minitweezers display extraordinary stability as compared to the first generation optical tweezers. A number of research groups in several countries use the Minitweezers in their single-molecule research 14,15,[34][35][36][37] . The details of construction, calibration, and operation of the device, including instruction videos, are available at the "Tweezers Lab" website (http://tweezerslab.unipr.it).…”

Section: Calibration and Operation Of Tweezersmentioning

confidence: 99%

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Stephenson

Wan

Tenenbaum

et al. 2014

JoVE

View full text Add to dashboard Cite

A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be increasingly important. As RNA function often depends on its ability to adopt alternative structures, it is difficult to predict RNA three-dimensional structures directly from sequence. Single-molecule approaches show potentials to solve the problem of RNA structural polymorphism by monitoring molecular structures one molecule at a time. This work presents a method to precisely manipulate the folding and structure of single RNA molecules using optical tweezers. First, methods to synthesize molecules suitable for single-molecule mechanical work are described. Next, various calibration procedures to ensure the proper operations of the optical tweezers are discussed. Next, various experiments are explained. To demonstrate the utility of the technique, results of mechanically unfolding RNA hairpins and a single RNA kissing complex are used as evidence. In these examples, the nanomanipulation technique was used to study folding of each structural domain, including secondary and tertiary, independently. Lastly, the limitations and future applications of the method are discussed. Video LinkThe video component of this article can be found at

show abstract

The Ribosome Modulates Nascent Protein Folding

Cited by 274 publications

References 62 publications

Effects of ribosomal exit tunnel on protein's cotranslational folding

Effects of ribosomal exit tunnel on protein's cotranslational folding

Structural entanglements in protein complexes

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Contact Info

Product

Resources

About