1
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Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023; 127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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Affiliation(s)
- Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden,(M.A.)
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06129 Halle (Saale), Germany,(U.W.)
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2
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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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3
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Singh A, Rief M, Žoldák G. Direct observation of chemo-mechanical coupling in DnaK by single-molecule force experiments. Biophys J 2022; 121:4729-4739. [PMID: 36196054 PMCID: PMC9748191 DOI: 10.1016/j.bpj.2022.09.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022] Open
Abstract
Protein allostery requires a communication channel for functional regulation between distal sites within a protein. In the molecular chaperone Hsp70, a two-domain enzyme, the ATP/ADP status of an N-terminal nucleotide-binding domain regulates the substrate affinity of a C-terminal substrate-binding domain. Recently available three-dimensional structures of Hsp70 in ATP/ADP states have provided deep insights into molecular pathways of allosteric signals. However, direct mechanical probing of long-range allosteric coupling between the ATP hydrolysis step and domain states is missing. Using laser optical tweezers, we examined the mechanical properties of a truncated two-domain DnaK(1-552ye) in apo/ADP/ATP- and peptide-bound states. We find that in the apo and ADP states, DnaK domains are mechanically stable and rigid. However, in the ATP state, substrate-binding domain (SBD)∗ye is mechanically destabilized as the result of interdomain docking followed by the unfolding of the α-helical lid. By observing the folding state of the SBD, we could observe the continuous ATP/ADP cycling of the enzyme in real time with a single molecule. The SBD lid closure is strictly coupled to the chemical steps of the ATP hydrolysis cycle even in the presence of peptide substrate.
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Affiliation(s)
- Anubhuti Singh
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany
| | - Matthias Rief
- Center for Functional Protein Assemblies (CPA), Physik Department, Technische Universität München, Garching, Germany.
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia; Center for Interdisciplinary Biosciences, Cassovia New Industry Cluster (CNIC), Trieda SNP 1, 040 11, Košice, Slovakia.
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4
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Dreydoppel M, Akke M, Weininger U. Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms. J Phys Chem B 2022; 126:7950-7956. [PMID: 36180044 PMCID: PMC9574926 DOI: 10.1021/acs.jpcb.2c05097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Aromatic ring flips are a hallmark of protein dynamics.
They are
experimentally studied by NMR spectroscopy, where recent advances
have led to improved characterization across a wide range of time
scales. Results on different proteins have been interpreted as continuous
diffusive ring rotations or jumplike flips, leading to diverging views
of the protein interior as being fluidlike or solidlike, respectively.
It is challenging to distinguish between these mechanisms and other
types of conformational exchange because chemical-shift-mediated line
broadening provides only conclusive evidence for ring flips only if
the system can be moved from the slow- to intermediate/fast-exchange
regime. Moreover, whenever the chemical shift difference between the
two symmetry-related sites is close to zero, it is not generally possible
to determine the exchange time scale. Here we resolve these issues
by measuring residual dipolar coupling (RDC)-mediated exchange contributions
using NMR relaxation dispersion experiments on proteins dissolved
in dilute liquid crystalline media. Excellent agreement is found between
the experimental difference in RDC between the two symmetry-related
sites and the value calculated from high-resolution X-ray structures,
demonstrating that dynamics measured for F52 in the B1 domain of protein
G reports on distinct, jumplike flips rather than other types of conformational
exchange.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, SE-22100Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120Halle (Saale), Germany
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5
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Mariño Pérez L, Ielasi FS, Bessa LM, Maurin D, Kragelj J, Blackledge M, Salvi N, Bouvignies G, Palencia A, Jensen MR. Visualizing protein breathing motions associated with aromatic ring flipping. Nature 2022; 602:695-700. [PMID: 35173330 PMCID: PMC8866124 DOI: 10.1038/s41586-022-04417-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/07/2022] [Indexed: 01/11/2023]
Abstract
Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold1-3. It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1. However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.
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Affiliation(s)
- Laura Mariño Pérez
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Departament de Química, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francesco S Ielasi
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Luiza M Bessa
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Damien Maurin
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Jaka Kragelj
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules (LBM), Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
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Dreydoppel M, Lichtenecker RJ, Akke M, Weininger U. 1H R 1ρ relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2021; 75:383-392. [PMID: 34510298 PMCID: PMC8642340 DOI: 10.1007/s10858-021-00382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H-13C spin pairs with vicinal 2H-12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H-13C/2H-12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s-1, and serve as a useful complement to previously developed 13C-based methods.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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7
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Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. JACS AU 2021; 1:833-842. [PMID: 34467336 PMCID: PMC8395657 DOI: 10.1021/jacsau.1c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 06/13/2023]
Abstract
Proteins are dynamic entities that intermittently depart from their ground-state structures and undergo conformational transitions as a critical part of their functions. Central to understanding such transitions are the structural rearrangements along the connecting pathway, where the transition state plays a special role. Using NMR relaxation at variable temperature and pressure to measure aromatic ring flips inside a protein core, we obtain information on the structure and thermodynamics of the transition state. We show that the isothermal compressibility coefficient of the transition state is similar to that of short-chain hydrocarbon liquids, implying extensive local unfolding of the protein. Our results further indicate that the required local volume expansions of the protein can occur not only with a net positive activation volume of the protein, as expected from previous studies, but also with zero activation volume by compaction of remote void volume, when averaged over the ensemble of states.
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Affiliation(s)
- Matthias Dreydoppel
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Britta Dorn
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
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8
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Karunanithy G, Shukla VK, Hansen DF. Methodological advancements for characterising protein side chains by NMR spectroscopy. Curr Opin Struct Biol 2021; 70:61-69. [PMID: 33989947 DOI: 10.1016/j.sbi.2021.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/18/2022]
Abstract
The surface of proteins is covered by side chains of polar amino acids that are imperative for modulating protein functionality through the formation of noncovalent intermolecular interactions. However, despite their tremendous importance, the unique structures of protein side chains require tailored approaches for investigation by nuclear magnetic resonance spectroscopy and so have traditionally been understudied compared with the protein backbone. Here, we review substantial recent methodological advancements within nuclear magnetic resonance spectroscopy to address this issue. Specifically, we consider advancements that provide new insight into methyl-bearing side chains, show the potential of using non-natural amino acids and reveal the actions of charged side chains. Combined, the new methods promise unprecedented characterisations of side chains that will further elucidate protein function.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.
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9
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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10
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Moinpour M, Barker NK, Guzman LE, Jewett JC, Langlais PR, Schwartz JC. Discriminating changes in protein structure using tyrosine conjugation. Protein Sci 2020; 29:1784-1793. [PMID: 32483864 DOI: 10.1002/pro.3897] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
Chemical modification of proteins has been crucial in engineering protein-based therapies, targeted biopharmaceutics, molecular probes, and biomaterials. Here, we explore the use of a conjugation-based approach to sense alternative conformational states in proteins. Tyrosine has both hydrophobic and hydrophilic qualities, thus allowing it to be positioned at protein surfaces, or binding interfaces, or to be buried within a protein. Tyrosine can be conjugated with 4-phenyl-3H-1,2,4-triazole-3,5(4H)-dione (PTAD). We hypothesized that individual protein conformations could be distinguished by labeling tyrosine residues in the protein with PTAD. We conjugated tyrosine residues in a well-folded protein, bovine serum albumin (BSA), and quantified labeled tyrosine with liquid chromatography with tandem mass spectrometry. We applied this approach to alternative conformations of BSA produced in the presence of urea. The amount of PTAD labeling was found to relate to the depth of each tyrosine relative to the protein surface. This study demonstrates a new use of tyrosine conjugation using PTAD as an analytic tool able to distinguish the conformational states of a protein.
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Affiliation(s)
- Mahta Moinpour
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Natalie K Barker
- Department of Medicine, Division of Endocrinology, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Lindsay E Guzman
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - John C Jewett
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Paul R Langlais
- Department of Medicine, Division of Endocrinology, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Jacob C Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
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