1
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Vugmeyster L, Ostrovsky D, Rodgers A, Gwin K, Smirnov SL, McKnight CJ, Fu R. Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR. Chemphyschem 2024; 25:e202300565. [PMID: 38175858 PMCID: PMC10922872 DOI: 10.1002/cphc.202300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/01/2023] [Indexed: 01/06/2024]
Abstract
Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Kirsten Gwin
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, WA 98225
| | - C. James McKnight
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL USA 32310
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2
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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3
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Rodgers A, Sawaged M, Ostrovsky D, Vugmeyster L. Effect of Cross-Seeding of Wild-Type Amyloid-β 1-40 Peptides with Post-translationally Modified Fibrils on Internal Dynamics of the Fibrils Using Deuterium Solid-State NMR. J Phys Chem B 2023; 127:2887-2899. [PMID: 36952330 PMCID: PMC10257444 DOI: 10.1021/acs.jpcb.2c07817] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Post-translationally modified (PTM) amyloid-β (Aβ) species can play an important role in modulating Alzheimer's disease pathology. These relatively less populated modifications can cross-seed the wild-type Aβ peptides to produce fibrils that retain many structural and functional features of the original PTM variants. We focus on studies of internal flexibility in the cross-seeded Aβ1-40 fibrils originating from seeding with two PTM variants with modifications in the disordered N-terminal domain: ΔE3 truncation and S8-phosphorylation. We employ an array of 2H solid-state NMR techniques, including line shape analysis over a broad temperature range, longitudinal relaxation, and quadrupolar CPMG, to assess the dynamics of the cross-seeded fibrils. The focus is placed on selected side-chain sites in the disordered N-terminal domain (G9 and V12) and hydrophobic core methyl and aromatic groups (L17, L34, M35, V36, and F19). We find that many of the essential features of the dynamics present in the original PTM seeds persist in the cross-seeded fibrils, and several of the characteristic features are even enhanced. This is particularly true for the activation energies of the rotameric motions and large-scale rearrangements of the N-terminal domain. Thus, our results on the dynamics complement prior structural and cell toxicity studies, suggesting that many PTM Aβ species can aggressively cross-seed the wild-type peptide in a manner that propagates the PTM's signature.
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Affiliation(s)
- Aryana Rodgers
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Matthew Sawaged
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
| | - Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
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4
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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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5
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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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6
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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
![]()
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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7
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Vugmeyster L, Au DF, Smith MC, Ostrovsky D. Comparative Hydrophobic Core Dynamics Between Wild-Type Amyloid-β Fibrils, Glutamate-3 Truncation, and Serine-8 Phosphorylation. Chemphyschem 2022; 23:e202100709. [PMID: 34837296 PMCID: PMC9484291 DOI: 10.1002/cphc.202100709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/10/2021] [Indexed: 02/06/2023]
Abstract
Post-translational modifications (PTMs) of amyloid-β (Aβ) species are implicated in the modulation of overall toxicities and aggregation propensities. We investigated the internal dynamics in the hydrophobic core of the truncated ΔE3 mutant fibrils of Aβ1-40 and compared them with prior and new data for wild-type fibrils as well as with phosphorylated S8 fibrils. Deuteron static solid-state NMR techniques, spanning line-shape analysis, longitudinal relaxation, and chemical exchange saturation transfer methods, were employed to assess the rotameric jumps of several methyl-bearing and aromatic groups in the core of the fibrils. Taken together, the results indicate the rather significant influence of the PTMs on the hydrophobic core dynamics, which propagates far beyond the local site of the chemical modification. The phosphorylated S8 fibrils display an overall rigidifying of the core based on the higher activation barriers of motions than the wild-type fibrils, whereas the ΔE3 fibrils induce a broader variety of changes, some of which are thermodynamic in nature rather than the kinetic ones.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204, corresponding author
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Matthew C. Smith
- Department of Chemistry, University of Colorado Denver, Denver CO USA 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver CO USA 80204
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8
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Vugmeyster L, Au DF, Ostrovsky D, Rickertsen DRL, Reed SM. Dynamics of Serine-8 Side-Chain in Amyloid-β Fibrils and Fluorenylmethyloxycarbonyl Serine Amino Acid, Investigated by Solid-State Deuteron NMR. J Phys Chem B 2020; 124:4723-4731. [PMID: 32396356 DOI: 10.1021/acs.jpcb.0c02490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Serine side-chains are strategic sites of post-translational modifications, and it is important to establish benchmarks of their internal dynamics. In this work, we compare the dynamics of serine side-chains in several biologically important systems: serine-8 in the disordered domain of Aβ1-40 fibrils in the hydrated and dry states and fluorenylmethyloxycarbonyl (Fmoc) serine with the bulky group that mimics the hydrophobicity of the fibril contacts yet lacks the complexity of the protein system. Using deuterium solid-state NMR static line shape and longitudinal relaxation techniques in the 310 to 180 K temperature range, we compare the main features of the dynamics in these systems. The main motional modes in the fibrils are large-scale fluctuations in the hydrated state of the fibrils as well as local motions such as 3-site jumps of the Cβ deuterons at high temperatures and small-angle fluctuations of the Cα-Cβ axis at low temperatures. In the hydrated fibrils, two distinct states are present with vastly different extents of large-scale diffusive motions and 3-site-jump rate constants. The hydrated state at the physiological conditions is dominated by the "free" state undergoing large-scale diffusive motions and very fast local 3-site jumps, while in the "bound" state, these large-scale motions are quenched due to transient inter- and intramolecular interactions. Additionally, in the bound state, the 3-site-jump motions are orders of magnitude slower. Details of the dynamics in the serine side-chain are dependent on fine structural features and hydration levels of the systems.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, United States
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, United States
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, Colorado 80204, United States
| | | | - Scott M Reed
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80204, United States
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9
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Emani PS, Yimer YY, Davidowski SK, Gebhart RN, Ferreira HE, Kuprov I, Pfaendtner J, Drobny GP. Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates. J Phys Chem B 2019; 123:10915-10929. [PMID: 31769684 DOI: 10.1021/acs.jpcb.9b09245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic MD trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure the R1 relaxation rates of uniformly 13C-labeled and site-specific 2H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal the following: (a) for the incoherent component of 13C relaxation, the nearest-neighbor spin interactions dominate, while the 1H-1H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine Cγ-Cδ bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the 2H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the Cβ and Cα nuclei; and (d) 13C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Yeneneh Y Yimer
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Stephen K Davidowski
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Rachel N Gebhart
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Helen E Ferreira
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Ilya Kuprov
- Department of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , U.K
| | - Jim Pfaendtner
- Department of Chemical Engineering , University of Washington , 105 Benson Hall, Box 351750 , Seattle , Washington 98195-1750 , United States
| | - Gary P Drobny
- Department of Chemistry , University of Washington , Box 351700 , Seattle , Washington 98195-1700 , United States
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10
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Meirovitch E, Freed JH. Local ordering and dynamics in anisotropic media by magnetic resonance: from liquid crystals to proteins. LIQUID CRYSTALS 2019; 47:1926-1954. [PMID: 32435078 PMCID: PMC7239324 DOI: 10.1080/02678292.2019.1622158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Indexed: 06/11/2023]
Abstract
Magnetic resonance methods have been used extensively for over 50 years to elucidate molecular structure and dynamics of liquid crystals (LCs), providing information quite unique in its rigour and extent. The ESR- or NMR-active probe is often a solute molecule reporting on characteristics associated with the surrounding (LC) medium, which exerts the spatial restrictions on the probe. The theoretical approaches developed for LCs are applicable to anisotropic media in general. Of particular interest is the interior space of a globular protein labelled, e.g. with a nitroxide moiety or a 15N-1H bond. The ESR or NMR label plays the role of the probe and the internal protein surroundings the role of the anisotropic medium. A general feature of the restricted motions is the local ordering, i.e. the nature, magnitude and symmetry of the spatial restraints exerted at the site of the moving probe. This property is the main theme of the present review article. We outline its treatment in our work from both the theoretical and the experimental points of view, highlighting the new physical insights gained. Our illustrations include studies on thermotropic (nematic and smectic) and lyotropic liquid crystals formed by phospholipids, in addition to studies of proteins.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
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11
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Meirovitch E, Liang Z, Freed JH. Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective. J Phys Chem B 2018; 122:8675-8684. [PMID: 30141954 DOI: 10.1021/acs.jpcb.8b06330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a potential, u, and the "local geometry" by the relative orientation of the model-related and nuclear magnetic resonance-related tensors. Here, we apply MOMD to phenyl-ring dynamics in several Αβ40-amyloid-fibrils, and the villin headpiece subdomain (HP36). Because the available data are limited in extent and sensitivity, we adjust u and R in the relevant parameter ranges, fixing the "local geometry" in accordance with standard stereochemistry. This yields a physically well-defined and consistent picture of phenyl-ring dynamics, enabling comparison between different systems. In the temperature range of 278-308 K, u has a strength of (1.7-1.8) kT and a rhombicity of (2.4-2.6) kT, and R has components of 5.0 × 102 ≤ R⊥ ≤ 2.0 × 103 s-1 and 6.3 × 105 ≤ R∥ ≤ 2.0 × 106 s-1. At 278 K, fibril hydration increases the axiality of both u and R; HP36 hydration has a similar effect at 295 K, reducing R⊥ considerably. The D23N mutation slows down the motion of the probe; Aβ40 polymorphism affects both this motion and the related local potential. The present study identifies the impact of various factors on phenyl-ring mobility in amyloid fibrils and globular proteins; the difference between the two protein forms is considerable. The distinctive impact of hydration on phenyl-ring motion and previously studied methyl-group motion is also examined. The 2H lineshapes considered here were analyzed previously with various multi-simple-mode (MSM) models, where several simple motional modes are combined. The MOMD and MSM interpretations differ in essence.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat-Gan 5290002 , Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
| | - Jack H Freed
- Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States
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12
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Vugmeyster L, Ostrovsky D. Basic experiments in 2H static NMR for the characterization of protein side-chain dynamics. Methods 2018; 148:136-145. [PMID: 29705208 PMCID: PMC6133770 DOI: 10.1016/j.ymeth.2018.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/02/2018] [Accepted: 04/24/2018] [Indexed: 12/23/2022] Open
Abstract
The focus of this review is the basic methodology for applications of static deuteron NMR for studies of dynamics in the side chains of proteins. We review experimental approaches for the measurements of static line shapes and relaxation rates as well as signal enhancement strategies using the multiple echo acquisition scheme. Further, we describe computational strategies for modeling jump and diffusive motions underlying experimental data. Applications are chosen from studies of amyloid fibrils comprising the amyloid-β protein.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO 80204, USA.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO 80204, USA
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13
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Ylinen EE, Punkkinen M, Birczyński A, Lalowicz ZT. Acetone mobility in zeolite cages with new features in the deuteron NMR spectra and relaxation. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 93:7-15. [PMID: 29803916 DOI: 10.1016/j.ssnmr.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/16/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
We studied deuteron NMR spectra and spin-lattice relaxation of deuterated acetone-d6, adsorbed into zeolites NaX (1.3) and NaY(2.4) at 100% coverage of sodium cations. At temperatures roughly below 160 K the deuterons are localized and their NMR characteristics are determined by CD3 rotation and rotational oscillations of acetone molecules. In NaX the CD3 rotation and rotational oscillations about the twofold axis of acetone dominate the spectra below 100 K, while above it oscillations also about other axes become important. In NaY dominant features are related to methyl tunnelling and to a smaller extent to rigid acetones, before the rotational oscillations about twofold axis start to prevail above 40 K. The analysis of the strongly non-exponential magnetization recovery was done by applying the recently introduced method (Ylinen et al., 2015 [12]), improved here to take into account the limited fast recovery at the level crossings, 10% at ωt=ω0 and 28% at ωt=2ω0. At first the experimental recovery is fitted by three exponentials with adjustable weights and decay rates. Then these quantities are calculated from activation energy distributions and known expressions for the deuteron relaxation rate. In NaY two distinctly separate activation energy distributions were needed, the dominant one being very broad. The use of three distributions, two of them covering practically the same energies as the broad one, lead to a somewhat better agreement with experiment. In general the theoretical results agree with experiment within experimental scatter. As the final result the mean activation energies and widths are obtained for activation energy distributions.
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Affiliation(s)
- E E Ylinen
- Wihuri Physical Laboratory, Department of Physics and Astronomy, University of Turku, FI-20014, Turku, Finland.
| | - M Punkkinen
- Wihuri Physical Laboratory, Department of Physics and Astronomy, University of Turku, FI-20014, Turku, Finland
| | - A Birczyński
- H. Niewodniczański Institute of Nuclear Physics of PAS, ul. Radzikowskiego 152, 31-342, Kraków, Poland
| | - Z T Lalowicz
- H. Niewodniczański Institute of Nuclear Physics of PAS, ul. Radzikowskiego 152, 31-342, Kraków, Poland
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14
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Vugmeyster L, Ostrovsky D. Comparative Dynamics of Methionine Side-Chain in FMOC-Methionine and in Amyloid Fibrils. Chem Phys Lett 2017; 673:108-112. [PMID: 28959059 DOI: 10.1016/j.cplett.2017.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, 1201 Larimer Street, University of Colorado at Denver, Denver, CO 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, 1201 Larimer Street, University of Colorado at Denver, Denver, CO 80204, USA
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Vugmeyster L, Ostrovsky D, Hoatson GL, Qiang W, Falconer IB. Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by 2H NMR Relaxation. J Phys Chem B 2017; 121:7267-7275. [PMID: 28699757 PMCID: PMC5567839 DOI: 10.1021/acs.jpcb.7b04726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures. The crossover temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate π-flips. Further, crossover temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, CO 80204
| | - Gina L. Hoatson
- Department of Physics, College of William and Mary, Williamsburg, Virginia, 23187
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, NY 13902
| | - Isaac B. Falconer
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
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Vugmeyster L, Ostrovsky D. Static solid-state 2H NMR methods in studies of protein side-chain dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:1-17. [PMID: 28844219 PMCID: PMC5576518 DOI: 10.1016/j.pnmrs.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 05/27/2023]
Abstract
In this review, we discuss the experimental static deuteron NMR techniques and computational approaches most useful for the investigation of side-chain dynamics in protein systems. Focus is placed on the interpretation of line shape and relaxation data within the framework of motional modeling. We consider both jump and diffusion models and apply them to uncover glassy behaviors, conformational exchange and dynamical transitions in proteins. Applications are chosen from globular and membrane proteins, amyloid fibrils, peptide adsorbed on surfaces and proteins specific to connective tissues.
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Adiram-Filiba N, Schremer A, Ohaion E, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Goobes G. Ubiquitin immobilized on mesoporous MCM41 silica surfaces - Analysis by solid-state NMR with biophysical and surface characterization. Biointerphases 2017; 12:02D414. [PMID: 28565916 PMCID: PMC5451314 DOI: 10.1116/1.4983273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/16/2022] Open
Abstract
Deriving the conformation of adsorbed proteins is important in the assessment of their functional activity when immobilized. This has particularly important bearings on the design of contemporary and new encapsulated enzyme-based drugs, biosensors, and other bioanalytical devices. Solid-state nuclear magnetic resonance (NMR) measurements can expand our molecular view of proteins in this state and of the molecular interactions governing protein immobilization on popular biocompatible surfaces such as silica. Here, the authors study the immobilization of ubiquitin on the mesoporous silica MCM41 by NMR and other techniques. Protein molecules are shown to bind efficiently at pH 5 through electrostatic interactions to individual MCM41 particles, causing their agglutination. The strong attraction of ubiquitin to MCM41 surface is given molecular context through evidence of proximity of basic, carbonyl and polar groups on the protein to groups on the silica surface using NMR measurements. The immobilized protein exhibits broad peaks in two-dimensional 13C dipolar-assisted rotational resonance spectra, an indication of structural multiplicity. At the same time, cross-peaks related to Tyr and Phe sidechains are missing due to motional averaging. Overall, the favorable adsorption of ubiquitin to MCM41 is accompanied by conformational heterogeneity and by a major loss of motional degrees of freedom as inferred from the marked entropy decrease. Nevertheless, local motions of the aromatic rings are retained in the immobilized state.
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Affiliation(s)
| | - Avital Schremer
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Eli Ohaion
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
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Donovan MA, Lutz H, Yimer YY, Pfaendtner J, Bonn M, Weidner T. LK peptide side chain dynamics at interfaces are independent of secondary structure. Phys Chem Chem Phys 2017; 19:28507-28511. [DOI: 10.1039/c7cp05897g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Real-time observation of the ultrafast motions of leucine side chains within model peptides at the water–air interface with representative folds – α-helix, 310-helix, β-strand – show that interfacial dynamics are mostly determined by surface interactions.
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Affiliation(s)
| | - Helmut Lutz
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Yeneneh Y. Yimer
- Department of Chemical Engineering
- University of Washington
- 105 Benson Hall
- Seattle
- USA
| | - Jim Pfaendtner
- Department of Chemical Engineering
- University of Washington
- 105 Benson Hall
- Seattle
- USA
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
- Department of Chemical Engineering
- University of Washington
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Vugmeyster L, Ostrovsky D, Clark MA, Falconer IB, Hoatson GL, Qiang W. Fast Motions of Key Methyl Groups in Amyloid-β Fibrils. Biophys J 2016; 111:2135-2148. [PMID: 27851938 PMCID: PMC5113154 DOI: 10.1016/j.bpj.2016.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/18/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, Colorado
| | - Matthew A Clark
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska
| | - Isaac B Falconer
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado
| | - Gina L Hoatson
- Department of Physics, College of William and Mary, Williamsburg, Virginia
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York
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