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Journal articles on the topic 'Protein folding studies'

Author: Grafiati

Published: 4 June 2021

Last updated: 8 February 2022

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1

Baker, David. "Protein folding, structure prediction and design." Biochemical Society Transactions 42, no. 2 (March 20, 2014): 225–29. http://dx.doi.org/10.1042/bst20130055.

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I describe how experimental studies of protein folding have led to advances in protein structure prediction and protein design. I describe the finding that protein sequences are not optimized for rapid folding, the contact order–protein folding rate correlation, the incorporation of experimental insights into protein folding into the Rosetta protein structure production methodology and the use of this methodology to determine structures from sparse experimental data. I then describe the inverse problem (protein design) and give an overview of recent work on designing proteins with new structures and functions. I also describe the contributions of the general public to these efforts through the Rosetta@home distributed computing project and the FoldIt interactive protein folding and design game.

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2

Bustamante, Carlos, Lisa Alexander, Kevin Maciuba, and Christian M. Kaiser. "Single-Molecule Studies of Protein Folding with Optical Tweezers." Annual Review of Biochemistry 89, no. 1 (June 20, 2020): 443–70. http://dx.doi.org/10.1146/annurev-biochem-013118-111442.

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Manipulation of individual molecules with optical tweezers provides a powerful means of interrogating the structure and folding of proteins. Mechanical force is not only a relevant quantity in cellular protein folding and function, but also a convenient parameter for biophysical folding studies. Optical tweezers offer precise control in the force range relevant for protein folding and unfolding, from which single-molecule kinetic and thermodynamic information about these processes can be extracted. In this review, we describe both physical principles and practical aspects of optical tweezers measurements and discuss recent advances in the use of this technique for the study of protein folding. In particular, we describe the characterization of folding energy landscapes at high resolution, studies of structurally complex multidomain proteins, folding in the presence of chaperones, and the ability to investigate real-time cotranslational folding of a polypeptide.

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3

Lu, Diannan, and Zheng Liu. "Studies of protein folding pathways." Annual Reports Section "C" (Physical Chemistry) 106 (2010): 259. http://dx.doi.org/10.1039/b903487k.

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4

Freisner, R. A., and J. R. Gunn. "Computational Studies of Protein Folding." Annual Review of Biophysics and Biomolecular Structure 25, no. 1 (June 1996): 315–42. http://dx.doi.org/10.1146/annurev.bb.25.060196.001531.

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5

Skolnick, J., and A. Kolinski. "Computational studies of protein folding." Computing in Science and Engineering 3, no. 5 (September 2001): 40–50. http://dx.doi.org/10.1109/mcise.2001.947107.

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6

Doerr, Allison. "Protein folding studies go global." Nature Methods 14, no. 9 (September 2017): 834. http://dx.doi.org/10.1038/nmeth.4418.

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7

Skolnick, J., and A. Kolinski. "Computational studies of protein folding." Computing in Science & Engineering 3, no. 3 (2001): 40–50. http://dx.doi.org/10.1109/5992.919264.

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8

Hanazono, Yuya, Kazuki Takeda, and Kunio Miki. "Crystallographic studies for the folding of an extending peptide." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1150. http://dx.doi.org/10.1107/s2053273314088494.

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Full-length proteins can fold into thermodynamically stable structures at an exceptionally fast rate as shown by in vitro experiments. In contrast, it takes much more time to finish nascent protein folding than full-length protein folding, because nascent protein folding depends on the rate of ribosome biosynthesis in the living cell. Therefore nascent polypeptide chains in vivo fold co-translationally in different manners from the full-length proteins. However, the transient structures and the co-translational folding pathway are not well understood. In order to reveal the atomic details of nascent protein folding, we studied the hPin1 WW domain, which consists of two beta-hairpins between the three-stranded beta-sheets. Here we report a series of WW domain N-terminal fragment structures with increasing amino acid length by using circular dichroism spectroscopy and X-ray crystallography. In crystallization, maltose-binding protein was fused just behind the WW domain fragments to fix the C-terminus as nascent proteins are anchored to the ribosome. Co-translational folding of beta-sheet-rich proteins is discussed based on our finding that intermediate-length fragments unexpectedly take a helical conformation, even though the full-length protein has no helical regions. Furthermore, in a region of one of the loop structures of the full-length protein, these fragments take different formations. Our results suggest that the newly synthesized polypeptides adopt the most stable conformation during the course of peptide extension and fold into the native structures, eventually.

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9

Dodson, C. A., N. Ferguson, T. J. Rutherford, C. M. Johnson, and A. R. Fersht. "Engineering a two-helix bundle protein for folding studies." Protein Engineering Design and Selection 23, no. 5 (February 3, 2010): 357–64. http://dx.doi.org/10.1093/protein/gzp080.

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10

Borgia, Alessandro, Philip M. Williams, and Jane Clarke. "Single-Molecule Studies of Protein Folding." Annual Review of Biochemistry 77, no. 1 (June 2008): 101–25. http://dx.doi.org/10.1146/annurev.biochem.77.060706.093102.

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11

Mallam, Anna L., and Sophie E. Jackson. "Folding Studies on a Knotted Protein." Journal of Molecular Biology 346, no. 5 (March 2005): 1409–21. http://dx.doi.org/10.1016/j.jmb.2004.12.055.

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12

Dadlez, M. "Disulfide bonds in protein folding studies: friends or foes?" Acta Biochimica Polonica 44, no. 3 (September 30, 1997): 433–52. http://dx.doi.org/10.18388/abp.1997_4395.

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The studies on protein folding pathways utilizing disulfide bonds as reporter groups in several protein model systems are reviewed. Implications for a general mechanism of protein folding are discussed. An updated folding pathway for bovine pancreatic trypsin inhibitor (BPTI) based on recent data is proposed.

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13

Dubey, Vikash Kumar, Monu Pande, and M. Jagannadham. "Snapshots of Protein Folding Problem: Implications of Folding and Misfolding Studies." Protein & Peptide Letters 13, no. 9 (September 1, 2006): 883–88. http://dx.doi.org/10.2174/092986606778256117.

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14

Lattman, Eaton Edward. "Small angle scattering studies of protein folding." Current Opinion in Structural Biology 4, no. 1 (January 1994): 87–92. http://dx.doi.org/10.1016/s0959-440x(94)90064-7.

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15

Capaldi, Andrew P., and Sheena E. Radford. "Kinetic studies of β-sheet protein folding." Current Opinion in Structural Biology 8, no. 1 (February 1998): 86–92. http://dx.doi.org/10.1016/s0959-440x(98)80014-6.

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16

van Nuland, Nico A. J., Vincent Forge, Jochen Balbach, and Christopher M. Dobson. "Real-Time NMR Studies of Protein Folding." Accounts of Chemical Research 31, no. 11 (November 1998): 773–80. http://dx.doi.org/10.1021/ar970079l.

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17

Karplus, Martin, and Andrej Šali. "Theoretical studies of protein folding and unfolding." Current Opinion in Structural Biology 5, no. 1 (February 1995): 58–73. http://dx.doi.org/10.1016/0959-440x(95)80010-x.

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18

Liu, Kaixian, and Christian Kaiser. "Single-Molecule Studies of Multidomain Protein Folding." Biophysical Journal 108, no. 2 (January 2015): 521a. http://dx.doi.org/10.1016/j.bpj.2014.11.2855.

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19

Li, Ruifang, Hong Li, Sarula Yang, and Xue Feng. "The Influences of Palindromes in mRNA on Protein Folding Rates." Protein & Peptide Letters 27, no. 4 (March 17, 2020): 303–12. http://dx.doi.org/10.2174/0929866526666191014144015.

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Background: It is currently believed that protein folding rates are influenced by protein structure, environment and temperature, amino acid sequence and so on. We have been working for long to determine whether and in what ways mRNA affects the protein folding rate. A large number of palindromes aroused our attention in our previous research. Whether these palindromes do have important influences on protein folding rates and what’s the mechanism? Very few related studies are focused on these problems. Objective: In this article, our motivation is to find out if palindromes have important influences on protein folding rates and what’s the mechanism. Method: In this article, the parameters of the palindromes were defined and calculated, the linear regression analysis between the values of each parameter and the experimental protein folding rates were done. Furthermore, to compare the results of different kinds of proteins, proteins were classified into the two-state proteins and the multi-state proteins. For the two kinds of proteins, the above linear regression analysis were performed respectively. Results : Protein folding rates were negatively correlated to the palindrome frequencies for all proteins. An extremely significant negative linear correlation appeared in the relationship between palindrome densities and protein folding rates. And the repeatedly used bases by different palindromes simultaneously have an important effect on the relationship between palindrome density and protein folding rate. Conclusion: The palindromes have important influences on protein folding rates, and the repeatedly used bases in different palindromes simultaneously play a key role in influencing the protein folding rates.

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20

Zhang, Hong, Weibin Gong, Si Wu, and Sarah Perrett. "Studying protein folding in health and disease using biophysical approaches." Emerging Topics in Life Sciences 5, no. 1 (March 4, 2021): 29–38. http://dx.doi.org/10.1042/etls20200317.

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Protein folding is crucial for normal physiology including development and healthy aging, and failure of this process is related to the pathology of diseases including neurodegeneration and cancer. Early thermodynamic and kinetic studies based on the unfolding and refolding equilibrium of individual proteins in the test tube have provided insight into the fundamental principles of protein folding, although the problem of predicting how any given protein will fold remains unsolved. Protein folding within cells is a more complex issue than folding of purified protein in isolation, due to the complex interactions within the cellular environment, including post-translational modifications of proteins, the presence of macromolecular crowding in cells, and variations in the cellular environment, for example in cancer versus normal cells. Development of biophysical approaches including fluorescence resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) techniques and cellular manipulations including microinjection and insertion of noncanonical amino acids has allowed the study of protein folding in living cells. Furthermore, biophysical techniques such as single-molecule fluorescence spectroscopy and optical tweezers allows studies of simplified systems at the single molecular level. Combining in-cell techniques with the powerful detail that can be achieved from single-molecule studies allows the effects of different cellular components including molecular chaperones to be monitored, providing us with comprehensive understanding of the protein folding process. The application of biophysical techniques to the study of protein folding is arming us with knowledge that is fundamental to the battle against cancer and other diseases related to protein conformation or protein–protein interactions.

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21

Hidaka, Yuji, and Shigeru Shimamoto. "Folding of peptides and proteins: role of disulfide bonds, recent developments." BioMolecular Concepts 4, no. 6 (December 1, 2013): 597–604. http://dx.doi.org/10.1515/bmc-2013-0022.

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AbstractDisulfide-containing proteins are ideal models for studies of protein folding as the folding intermediates can be observed, trapped, and separated by HPLC during the folding reaction. However, regulating or analyzing the structures of folding intermediates of peptides and proteins continues to be a difficult problem. Recently, the development of several techniques in peptide chemistry and biotechnology has resulted in the availability of some powerful tools for studying protein folding in the context of the structural analysis of native, mutant proteins, and folding intermediates. In this review, recent developments in the field of disulfide-coupled peptide and protein folding are discussed, from the viewpoint of chemical and biotechnological methods, such as analytical methods for the detection of disulfide pairings, chemical methods for disulfide bond formation between the defined Cys residues, and applications of diselenide bonds for the regulation of disulfide-coupled peptide and protein folding.

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22

MIZUGUCHI, Mineyuki, and Chiaki NISHIMURA. "Studies of Protein Folding in Wright/Dyson Laboratory." Seibutsu Butsuri 41, no. 4 (2001): 208–10. http://dx.doi.org/10.2142/biophys.41.208.

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23

Shakhnovich, Eugene I. "Theoretical studies of protein-folding thermodynamics and kinetics." Current Opinion in Structural Biology 7, no. 1 (February 1997): 29–40. http://dx.doi.org/10.1016/s0959-440x(97)80005-x.

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24

Kataoka, Mikio, and Yuji Goto. "X-ray solution scattering studies of protein folding." Folding and Design 1, no. 5 (October 1996): R107—R114. http://dx.doi.org/10.1016/s1359-0278(96)00047-8.

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25

Neira, José Luis, and Manuel Rico. "Folding studies on ribonuclease A, a model protein." Folding and Design 2, no. 1 (February 1997): R1—R11. http://dx.doi.org/10.1016/s1359-0278(97)00001-1.

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26

Dyer, R. Brian, Feng Gai, William H. Woodruff, Rudolf Gilmanshin, and Robert H. Callender. "Infrared Studies of Fast Events in Protein Folding." Accounts of Chemical Research 31, no. 11 (November 1998): 709–16. http://dx.doi.org/10.1021/ar970343a.

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27

Shiu, Y. J., Catherlene Su, Y. L. Yeh, K. K. Liang, M. Hayashi, Yan Mo, Yijing Yan, and S. H. Lin. "Experimental and Theoretical Studies of Protein Folding-Unfolding." Journal of the Chinese Chemical Society 51, no. 5B (October 2004): 1161–73. http://dx.doi.org/10.1002/jccs.200400172.

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28

Dobson, Christopher M., and Peter J. Hore. "Kinetic studies of protein folding using NMR spectroscopy." Nature Structural Biology 5, no. 7 (July 1998): 504–7. http://dx.doi.org/10.1038/744.

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29

Wlodarski, Tomasz, Chris Waudby, Chan Sammy, Michele Vendruscolo, and John Christodoulou. "The Computational Studies of Co-Translational Protein Folding." Biophysical Journal 108, no. 2 (January 2015): 515a. http://dx.doi.org/10.1016/j.bpj.2014.11.2823.

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30

Vanhove, M., A. Lejeune, and R. H. Pain. "β-Lactamases as models for protein-folding studies." Cellular and Molecular Life Sciences CMLS 54, no. 4 (April 1998): 372–77. http://dx.doi.org/10.1007/s000180050166.

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31

Agostini, Flavia P., Diogo De O. Soares-Pinto, Marcelo A. Moret, Carla Osthoff, and Pedro G. Pascutti. "Generalized simulated annealing applied to protein folding studies." Journal of Computational Chemistry 27, no. 11 (2006): 1142–55. http://dx.doi.org/10.1002/jcc.20428.

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32

Clark, Nicola S., Ian Dodd, Danuta E. Mossakowska, Richard A. G. Smith, and Michael G. Gore. "Folding and conformational studies on SCR1-3 domains of human complement receptor 1." "Protein Engineering, Design and Selection" 9, no. 10 (1996): 877–84. http://dx.doi.org/10.1093/protein/9.10.877.

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33

Ekonomiuk, Dariusz, Marcin Kielbasinski, and Andrzej Kolinski. "Protein modeling with reduced representation: statistical potentials and protein folding mechanism." Acta Biochimica Polonica 52, no. 4 (May 31, 2005): 741–48. http://dx.doi.org/10.18388/abp.2005_3385.

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A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon beta-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the beta-sheet.

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34

Narayan, Mahesh. "Revisiting the Formation of a Native Disulfide Bond: Consequences for Protein Regeneration and Beyond." Molecules 25, no. 22 (November 16, 2020): 5337. http://dx.doi.org/10.3390/molecules25225337.

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Oxidative protein folding involves the formation of disulfide bonds and the regeneration of native structure (N) from the fully reduced and unfolded protein (R). Oxidative protein folding studies have provided a wealth of information on underlying physico-chemical reactions by which disulfide-bond-containing proteins acquire their catalytically active form. Initially, we review key events underlying oxidative protein folding using bovine pancreatic ribonuclease A (RNase A), bovine pancreatic trypsin inhibitor (BPTI) and hen-egg white lysozyme (HEWL) as model disulfide bond-containing folders and discuss consequential outcomes with regard to their folding trajectories. We re-examine the findings from the same studies to underscore the importance of forming native disulfide bonds and generating a “native-like” structure early on in the oxidative folding pathway. The impact of both these features on the regeneration landscape are highlighted by comparing ideal, albeit hypothetical, regeneration scenarios with those wherein a native-like structure is formed relatively “late” in the R→N trajectory. A special case where the desired characteristics of oxidative folding trajectories can, nevertheless, stall folding is also discussed. The importance of these data from oxidative protein folding studies is projected onto outcomes, including their impact on the regeneration rate, yield, misfolding, misfolded-flux trafficking from the endoplasmic reticulum (ER) to the cytoplasm, and the onset of neurodegenerative disorders.

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35

Oliveberg, Mikael, and Peter G. Wolynes. "The experimental survey of protein-folding energy landscapes." Quarterly Reviews of Biophysics 38, no. 3 (August 2005): 245–88. http://dx.doi.org/10.1017/s0033583506004185.

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1. Introduction 22. The macroscopic and microscopic views of protein folding 22.1 The macroscopic view: the experimental folding free-energy profile 22.2 The microscopic view: an underlying energy landscape 33. The micro to macro projection: from an energy landscape to a free-energy profile 64. Global features of the protein folding transition-state ensemble 124.1 Overall transition state location β[Dagger]: a measure of compactness 124.2 What makes folding so robust ? 135. Structural characterization of the transition-state ensemble 165.1 Insights from ϕ-value analysis 166. Deviations from ideality 206.1 β[Dagger] shifts along seemingly robust trajectories 216.2 Anomalous ϕ values, frustration and inhomogeneities 257. Intermediates 288. Detours, traps and frustration 298.1 Premature collapse and non-native trapping 299. Diffusion on the energy landscape and the elementary events of protein folding 3010. Malleability of folding routes: changes of the dominant collective coordinates for folding 3311. The evolution of the shape of the energy landscape 3511.1 Negative design: the hidden dimension of the folding code 3512. Mechanistic multiplicity and evolutionary choice 3613. Acknowledgements 3714. References 38We review what has been learned about the protein-folding problem from experimental kinetic studies. These studies reveal patterns of both great richness and surprising simplicity. The patterns can be interpreted in terms of proteins possessing an energy landscape which is largely, but not completely, funnel-like. Issues such as speed limitations of folding, the robustness of folding, the origin of barriers and cooperativity and the ensemble nature of transition states, intermediate and traps are assessed using the results from several experimental groups highlighting energy-landscape ideas as an interpretive framework.

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36

Kuwajima, Kunihiro. "The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins." Biomolecules 10, no. 3 (March 6, 2020): 407. http://dx.doi.org/10.3390/biom10030407.

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From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms of protein folding. This article describes how the presence of the two types of folding behavior has been confirmed experimentally, and discusses the relationships between the two-state and the non-two-state folding reactions, on the basis of available data on the correlations of the folding rate constant with various structure-based properties, which are determined primarily by the backbone topology of proteins. Finally, a two-stage hierarchical model is proposed as a general mechanism of protein folding. In this model, protein folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the molten globule state as a folding intermediate. The two-state folding is thus merely a simplified version of the hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate.

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37

Farías-Rico, José Arcadio, Frida Ruud Selin, Ioanna Myronidi, Marie Frühauf, and Gunnar von Heijne. "Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome." Proceedings of the National Academy of Sciences 115, no. 40 (September 17, 2018): E9280—E9287. http://dx.doi.org/10.1073/pnas.1812756115.

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During the last five decades, studies of protein folding in dilute buffer solutions have produced a rich picture of this complex process. In the cell, however, proteins can start to fold while still attached to the ribosome (cotranslational folding) and it is not yet clear how the ribosome affects the folding of protein domains of different sizes, thermodynamic stabilities, and net charges. Here, by using arrest peptides as force sensors and on-ribosome pulse proteolysis, we provide a comprehensive picture of how the distance from the peptidyl transferase center in the ribosome at which proteins fold correlates with protein size. Moreover, an analysis of a large collection of mutants of theEscherichia coliribosomal protein S6 shows that the force exerted on the nascent chain by protein folding varies linearly with the thermodynamic stability of the folded state, and that the ribosome environment disfavors folding of domains of high net-negative charge.

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38

Marino, Jacopo, Reto Walser, Martin Poms, and Oliver Zerbe. "Understanding GPCR recognition and folding from NMR studies of fragments." RSC Advances 8, no. 18 (2018): 9858–70. http://dx.doi.org/10.1039/c8ra01520a.

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Cotranslational protein folding is a vectorial process, and for membrane proteins, N-terminal helical segments are the first that become available for membrane insertion. Here fragments corresponding to these segments are investigated by NMR.

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39

Kapatai, Georgia, Andrew Large, and Peter Lund. "Keeping proteins on the straight and narrow: Molecular chaperones in the Archaea." Biochemist 26, no. 3 (June 1, 2004): 22–25. http://dx.doi.org/10.1042/bio02603022.

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For many years, studies on protein folding were done by biochemists and biophysicists using purified components and defined conditions. More recently, attention has shifted to thinking about protein folding in the messier internal environment of the cell. Here, proteins are faced with many hazards not encountered in the test tube: other proteins are present at high concentrations, the cell is full of membranes that need to be crossed, and conditions that can have a large effect on protein folding may not be constant. Proteins are often not well suited for these vagaries of cellular life, and a host of accessory proteins need to be present to assist the process of protein folding. These accessory proteins are referred to as molecular chaperones, and they use various mechanisms to make sure that their client proteins stay on the straight and narrow path to the folded active state.

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40

Hertzog, David E., Xavier Michalet, Marcus Jäger, Xiangxu Kong, Juan G. Santiago, Shimon Weiss, and Olgica Bakajin. "Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding." Analytical Chemistry 76, no. 24 (December 2004): 7169–78. http://dx.doi.org/10.1021/ac048661s.

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41

Goldenberg, D. P. "Genetic Studies of Protein Stability and Mechanisms of Folding." Annual Review of Biophysics and Biophysical Chemistry 17, no. 1 (June 1988): 481–507. http://dx.doi.org/10.1146/annurev.bb.17.060188.002405.

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42

Hirst, Jonathan D., Samita Bhattacharjee, and Alexey V. Onufriev. "Theoretical studies of time-resolved spectroscopy of protein folding." Faraday Discussions 122 (July 16, 2002): 253–67. http://dx.doi.org/10.1039/b200714b.

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43

Frieden, Carl, Sydney D. Hoeltzli, and Ira J. Ropson. "NMR and protein folding: Equilibrium and stopped-flow studies." Protein Science 2, no. 12 (December 1993): 2007–14. http://dx.doi.org/10.1002/pro.5560021202.

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44

Moroder, Luis. "Studies of protein folding and structure with model peptides." Journal of Peptide Science 11, no. 5 (2005): 258–61. http://dx.doi.org/10.1002/psc.661.

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45

van Nuland, Nico A. J., Vincent Forge, Jochen Balbach, and Christopher M. Dobson. "ChemInform Abstract: Real-Time NMR Studies of Protein Folding." ChemInform 30, no. 5 (June 17, 2010): no. http://dx.doi.org/10.1002/chin.199905300.

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46

Serrano, Arnaldo L., Matthias M. Waegele, and Feng Gai. "Spectroscopic studies of protein folding: Linear and nonlinear methods." Protein Science 21, no. 2 (December 28, 2011): 157–70. http://dx.doi.org/10.1002/pro.2006.

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47

Kim, Judy. "Spectroscopic Studies of Membrane Protein Folding: Changes in Hydration." Biophysical Journal 106, no. 2 (January 2014): 33a. http://dx.doi.org/10.1016/j.bpj.2013.11.256.

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48

Leachman, Samuel M., Christian A. M. Wilson, Susan Marqusee, and Carlos Bustamante. "Protein-Folding Studies using Hybrid TIRF SmFRET-Magnetic Tweezers." Biophysical Journal 106, no. 2 (January 2014): 469a—470a. http://dx.doi.org/10.1016/j.bpj.2013.11.2657.

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49

Knowlton, Jonathan J., Daniel Gestaut, Boxue Ma, Gwen Taylor, Alpay Burak Seven, Alexander Leitner, Gregory J. Wilson, et al. "Structural and functional dissection of reovirus capsid folding and assembly by the prefoldin-TRiC/CCT chaperone network." Proceedings of the National Academy of Sciences 118, no. 11 (March 8, 2021): e2018127118. http://dx.doi.org/10.1073/pnas.2018127118.

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Intracellular protein homeostasis is maintained by a network of chaperones that function to fold proteins into their native conformation. The eukaryotic TRiC chaperonin (TCP1-ring complex, also called CCT for cytosolic chaperonin containing TCP1) facilitates folding of a subset of proteins with folding constraints such as complex topologies. To better understand the mechanism of TRiC folding, we investigated the biogenesis of an obligate TRiC substrate, the reovirus σ3 capsid protein. We discovered that the σ3 protein interacts with a network of chaperones, including TRiC and prefoldin. Using a combination of cryoelectron microscopy, cross-linking mass spectrometry, and biochemical approaches, we establish functions for TRiC and prefoldin in folding σ3 and promoting its assembly into higher-order oligomers. These studies illuminate the molecular dynamics of σ3 folding and establish a biological function for TRiC in virus assembly. In addition, our findings provide structural and functional insight into the mechanism by which TRiC and prefoldin participate in the assembly of protein complexes.

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Härd, Torleif. "NMR studies of protein–nucleic acid complexes: structures, solvation, dynamics and coupled protein folding." Quarterly Reviews of Biophysics 32, no. 1 (February 1999): 57–98. http://dx.doi.org/10.1017/s0033583599003509.

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Abstract:

Many basic events which concern management and manipulation of genes within a cell – for instance transcription, replication and recombination – rely on specific interactions between proteins and nucleic acids. Such interactions are also essential for many house-keeping functions, like packing and unpacking of DNA in chromatin and assembly of ribosomes. Moreover, the details of protein–nucleic acid interplay is essential for understanding the action of viruses. The list of functional mechanisms in biology that rely on protein–DNA and protein–RNA interactions can be made much longer, but these examples represent some of the topics which motivated structural biologists to study complexes between proteins and nucleic acids as a first step beyond structure determinations of individual biomolecules.

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