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Baxa MC, Sosnick TR. Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis. Methods Mol Biol 2022; 2376:31-63. [PMID: 34845602 DOI: 10.1007/978-1-0716-1716-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of the transition state ensemble (TSE) represents the rate-limiting step in protein folding. The TSE is the least populated state on the pathway, and its characterization remains a challenge. Properties of the TSE can be inferred from the effects on folding and unfolding rates for various perturbations. A difficulty remains on how to translate these kinetic effects to structural properties of the TSE. Several factors can obscure the translation of point mutations in the frequently used method, "mutational Phi analysis." We take a complementary approach in "Psi analysis," employing rationally inserted metal binding sites designed to probe pairwise contacts in the TSE. These contacts can be confidently identified and used to construct structural models of the TSE. The method has been applied to multiple proteins and consistently produces a considerably more structured and native-like TSE than Phi analysis. This difference has significant implications to our understanding of protein folding mechanisms. Here we describe the application of the method and discuss how it can be used to study other conformational transitions such as binding.
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Affiliation(s)
- Michael C Baxa
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
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Lin Q, Hopper D, Zhang H, Sfyris Qoon J, Shen Z, Karas JA, Hughes RA, Northfield SE. 1,3-Dichloroacetone: A Robust Reagent for Preparing Bicyclic Peptides. ACS OMEGA 2020; 5:1840-1850. [PMID: 32039320 PMCID: PMC7003203 DOI: 10.1021/acsomega.9b03152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
The chemical synthesis of cyclic peptides is a well-established area of research. This has been further expanded by development of bio-orthogonal reactions that enable access to peptides of greater structural complexity. One approach utilizes 1,3-dichloroacetone to selectively link free cysteine side-chains with an acetone-like bridge via an SN2 reaction. Here, we have used this reaction to dimerize cyclic peptide monomers to create novel bicyclic dimeric peptides. We investigated a range of reaction parameters to identify the optimal dimerization conditions for our model systems. One of the acetone-linked dimeric peptides was analyzed for proteolytic stability in human serum and was observed to still be fully intact after 48 h. This study provides valuable insights into the application of 1,3-dichloroacetone as a tool in the synthesis of complex, multicyclic peptides.
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Palyanov AY, Chekmarev SF. Hydrodynamic description of protein folding: the decrease of the probability fluxes as an indicator of transition states in two-state folders. J Biomol Struct Dyn 2017; 35:3152-3160. [DOI: 10.1080/07391102.2016.1248490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Andrey Yu. Palyanov
- Ershov Institute of Informatics Systems, SB RAS, Novosibirsk, 630090Russia
- Department of Natural Sciences, Novosibirsk State University, 630090Russia
| | - Sergei F. Chekmarev
- Institute of Thermophysics, SB RAS, 630090Russia
- Department of Physics, Novosibirsk State University, 630090Russia
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics. Curr Opin Struct Biol 2015; 36:1-9. [PMID: 26687767 DOI: 10.1016/j.sbi.2015.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 11/10/2015] [Indexed: 01/11/2023]
Abstract
Progress in our understanding of the simple folding dynamics of small proteins and the complex dynamics of large proteins is reviewed. Recent characterizations of the folding transition path of small proteins revealed a simple dynamics explainable by the native centric model. In contrast, the accumulated data showed the substates containing residual structures in the unfolded state and partially populated intermediates, causing complexity in the early folding dynamics of small proteins. The size of the unfolded proteins in the absence of denaturants is likely expanded but still controversial. The steady progress in the observation of folding of large proteins has clarified the rapid formation of long-range contacts that seem inconsistent with the native centric model, suggesting that the folding strategy of large proteins is distinct from that of small proteins.
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Assem N, Ferreira DJ, Wolan DW, Dawson PE. Acetone-Linked Peptides: A Convergent Approach for Peptide Macrocyclization and Labeling. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502607] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Assem N, Ferreira DJ, Wolan DW, Dawson PE. Acetone-Linked Peptides: A Convergent Approach for Peptide Macrocyclization and Labeling. Angew Chem Int Ed Engl 2015; 54:8665-8. [PMID: 26096515 DOI: 10.1002/anie.201502607] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Indexed: 11/09/2022]
Abstract
Macrocyclization is a broadly applied approach for overcoming the intrinsically disordered nature of linear peptides. Herein, it is shown that dichloroacetone (DCA) enhances helical secondary structures when introduced between peptide nucleophiles, such as thiols, to yield an acetone-linked bridge (ACE). Aside from stabilizing helical structures, the ketone moiety embedded in the linker can be modified with diverse molecular tags by oxime ligation. Insights into the structure of the tether were obtained through co-crystallization of a constrained S-peptide in complex with RNAse S. The scope of the acetone-linked peptides was further explored through the generation of N-terminus to side chain macrocycles and a new approach for generating fused macrocycles (bicycles). Together, these studies suggest that acetone linking is generally applicable to peptide macrocycles with a specific utility in the synthesis of stabilized helices that incorporate functional tags.
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Affiliation(s)
- Naila Assem
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA (USA)
| | - David J Ferreira
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA (USA)
| | - Dennis W Wolan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA (USA)
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA (USA).
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Adhikari AN, Freed KF, Sosnick TR. Simplified protein models: predicting folding pathways and structure using amino acid sequences. PHYSICAL REVIEW LETTERS 2013; 111:028103. [PMID: 23889448 PMCID: PMC4047675 DOI: 10.1103/physrevlett.111.028103] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Indexed: 06/02/2023]
Abstract
We demonstrate the ability of simultaneously determining a protein's folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or "foldons." Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.
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Affiliation(s)
- Aashish N. Adhikari
- Department of Chemistry, University of Chicago, Chicago, IL 60637 USA
- James Franck Institute, University of Chicago, Chicago, IL 60637 USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637 USA
| | - Karl F. Freed
- Department of Chemistry, University of Chicago, Chicago, IL 60637 USA
- James Franck Institute, University of Chicago, Chicago, IL 60637 USA
- Computation Institute, University of Chicago, Chicago, IL 60637 USA
| | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637 USA
- Computation Institute, University of Chicago, Chicago, IL 60637 USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637 USA
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Abstract
Equilibrium molecular dynamics simulations, in which proteins spontaneously and repeatedly fold and unfold, have recently been used to help elucidate the mechanistic principles that underlie the folding of fast-folding proteins. The extent to which the conclusions drawn from the analysis of such proteins, which fold on the microsecond timescale, apply to the millisecond or slower folding of naturally occurring proteins is, however, unclear. As a first attempt to address this outstanding issue, we examine here the folding of ubiquitin, a 76-residue-long protein found in all eukaryotes that is known experimentally to fold on a millisecond timescale. Ubiquitin folding has been the subject of many experimental studies, but its slow folding rate has made it difficult to observe and characterize the folding process through all-atom molecular dynamics simulations. Here we determine the mechanism, thermodynamics, and kinetics of ubiquitin folding through equilibrium atomistic simulations. The picture emerging from the simulations is in agreement with a view of ubiquitin folding suggested from previous experiments. Our findings related to the folding of ubiquitin are also consistent, for the most part, with the folding principles derived from the simulation of fast-folding proteins, suggesting that these principles may be applicable to a wider range of proteins.
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Affiliation(s)
| | | | - David E. Shaw
- D. E. Shaw Research, New York, NY 10036; and
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032
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