Probing the structural dynamics of proteins and nucleic acids with optical tweezers

Ritchie, Dustin B.; Woodside, Michael T.

doi:10.1016/j.sbi.2015.06.006

Cited by 114 publications

(82 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In summary, the single-molecule experiments of Ritchie and Woodside (18) and Woodside and Block (53) were finally able to measure the multiple parallel trajectories that anchor energy landscape considerations. The results show that trajectory multiplicity and variability do exist but the distribution of folding rates (Fig.…”

Section: Results and Considerationsmentioning

confidence: 99%

See 1 more Smart Citation

The case for defined protein folding pathways

Englander

Mayne

2017

Proc. Natl. Acad. Sci. U.S.A.

126

143

View full text Add to dashboard Cite

We consider the differences between the many-pathway protein folding model derived from theoretical energy landscape considerations and the defined-pathway model derived from experiment. A basic tenet of the energy landscape model is that proteins fold through many heterogeneous pathways by way of amino acid-level dynamics biased toward selecting native-like interactions. The many pathways imagined in the model are not observed in the structureformation stage of folding by experiments that would have found them, but they have now been detected and characterized for one protein in the initial prenucleation stage. Analysis presented here shows that these many microscopic trajectories are not distinct in any functionally significant way, and they have neither the structural information nor the biased energetics needed to select native vs. nonnative interactions during folding. The opposed defined-pathway model stems from experimental results that show that proteins are assemblies of small cooperative units called foldons and that a number of proteins fold in a reproducible pathway one foldon unit at a time. Thus, the same foldon interactions that encode the native structure of any given protein also naturally encode its particular foldon-based folding pathway, and they collectively sum to produce the energy bias toward native interactions that is necessary for efficient folding. Available information suggests that quantized native structure and stepwise folding coevolved in ancient repeat proteins and were retained as a functional pair due to their utility for solving the difficult protein folding problem.protein folding | foldons | energy landscape theory P rotein folding is among the most important reactions in all of biology. However, 50 y after C. B. Anfinsen showed that proteins can fold spontaneously without outside help (1, 2), and despite the intensive work of thousands of researchers leading to more than five publications per day in the current literature, there is still no general agreement on the most primary questions (3-5). How do proteins fold? Why do they fold in that way? How is the course of folding encoded in a 1D amino acid sequence? These questions have fundamental significance for protein science and its numerous applications. Over the years these questions have generated a large literature leading to different models for the folding process.The "new view" folding model, derived from hypothetical energy landscape and statistical mechanical considerations (6-12), proposes that folding proteins navigate to their native state through very many independent pathways. The many trajectories in Fig. 1A imply an unfolded protein conformationally searching for its lowestenergy native state by way of dynamic bond rotations in a way that is guided by its energy landscape, as for any chemical reaction. For effective performance, folding proteins must "know" how to select native as opposed to nonnative interactions. This information is said to be contained in the shape of the energy landscape, but how it is ...

show abstract

Section: Results and Considerationsmentioning

confidence: 99%

“…The numerous trajectories envisioned in the many-pathway model have been detected and characterized (18)(19)(20) and so can be considered on their merits rather than by abstract inference. Continued methods development (21,22) has enhanced the search for foldons and the investigation of their role in both equilibrium and kinetic folding (16,17).…”

mentioning

confidence: 99%

The case for defined protein folding pathways

Englander

Mayne

2017

Proc. Natl. Acad. Sci. U.S.A.

126

143

View full text Add to dashboard Cite

show abstract

“…In particular, the Woodside group has recently measured the duration and the shape of the transition paths connecting the folded and unfolded states. [25][26][27] Other techniques commonly used for SMFS studies include magnetic tweezers and Atomic Force Microscopy (AFM). The utility of the SMFS approach in biophysics is not limited to biomolecular folding; this approach has also been used, e.g., to study enzyme catalysis, 28 biopolymer elasticity, 29,30 molecular mechanisms of adhesion, 31 and the motion of molecular motors.…”

Section: Mechanochemistry Describes Phenomena Ranging From Frictiomentioning

confidence: 99%

Perspective: Mechanochemistry of biological and synthetic molecules

Makarov

2016

The Journal of Chemical Physics

116

View full text Add to dashboard Cite

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

show abstract

“…This is especially true for single-molecule force spectroscopy (SMFS), in which the extension of a protein is measured as its structure changes in response to a denaturing force applied to its ends. 40 SMFS has been used extensively to study the folding energy landscapes of both proteins and nucleic acids. 41 Because SMFS data capture the statistical mechanics of the structural fluctuations, they can be used to measure energy landscapes in greater detail than possible at the ensemble level.…”

Section: Energy Landscapes and Kinetics In Foldingmentioning

confidence: 99%

Comparing the energy landscapes for native folding and aggregation of PrP

Dee

Woodside

2016

Prion

View full text Add to dashboard Cite

Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.

show abstract

Probing the structural dynamics of proteins and nucleic acids with optical tweezers

Cited by 114 publications

References 87 publications

The case for defined protein folding pathways

The case for defined protein folding pathways

Perspective: Mechanochemistry of biological and synthetic molecules

Comparing the energy landscapes for native folding and aggregation of PrP

Contact Info

Product

Resources

About