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Menke FS, Mazzier D, Wicher B, Allmendinger L, Kauffmann B, Maurizot V, Huc I. Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds. Org Biomol Chem 2023; 21:1275-1283. [PMID: 36645374 DOI: 10.1039/d2ob02109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.
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Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Daniela Mazzier
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Lars Allmendinger
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (UMS3011/US001), CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
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Horowitz S, Koldewey P, Stull F, Bardwell JC. Folding while bound to chaperones. Curr Opin Struct Biol 2017; 48:1-5. [PMID: 28734135 DOI: 10.1016/j.sbi.2017.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
Chaperones are important in preventing protein aggregation and aiding protein folding. How chaperones aid protein folding remains a key question in understanding their mechanism. The possibility of proteins folding while bound to chaperones was reintroduced recently with the chaperone Spy, many years after the phenomenon was first reported with the chaperones GroEL and SecB. In this review, we discuss the salient features of folding while bound in the cases for which it has been observed and speculate about its biological importance and possible occurrence in other chaperones.
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Affiliation(s)
- Scott Horowitz
- Department of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80208, USA.
| | - Philipp Koldewey
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - Frederick Stull
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - James Ca Bardwell
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA.
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Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL, Bardwell JCA. Visualizing chaperone-assisted protein folding. Nat Struct Mol Biol 2016; 23:691-7. [PMID: 27239796 PMCID: PMC4937829 DOI: 10.1038/nsmb.3237] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 05/04/2016] [Indexed: 12/26/2022]
Abstract
Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.
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Affiliation(s)
- Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
| | - Loïc Salmon
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
| | - Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
| | - Logan S Ahlstrom
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Raoul Martin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Pavel V Afonine
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Henry van den Bedem
- Division of Biosciences, SLAC National Accelerator Laboratory, Stanford University, Stanford, California, USA
| | - Lili Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Laboratory, Menlo Park, California, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Charles L Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan, USA
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Howard Hughes Medical Institute, Ann Arbor, Michigan, USA
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Wolynes PG. Evolution, energy landscapes and the paradoxes of protein folding. Biochimie 2014; 119:218-30. [PMID: 25530262 DOI: 10.1016/j.biochi.2014.12.007] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/11/2014] [Indexed: 01/25/2023]
Abstract
Protein folding has been viewed as a difficult problem of molecular self-organization. The search problem involved in folding however has been simplified through the evolution of folding energy landscapes that are funneled. The funnel hypothesis can be quantified using energy landscape theory based on the minimal frustration principle. Strong quantitative predictions that follow from energy landscape theory have been widely confirmed both through laboratory folding experiments and from detailed simulations. Energy landscape ideas also have allowed successful protein structure prediction algorithms to be developed. The selection constraint of having funneled folding landscapes has left its imprint on the sequences of existing protein structural families. Quantitative analysis of co-evolution patterns allows us to infer the statistical characteristics of the folding landscape. These turn out to be consistent with what has been obtained from laboratory physicochemical folding experiments signaling a beautiful confluence of genomics and chemical physics.
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Affiliation(s)
- Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
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Abstract
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology.
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