1
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Salamh S, Sayyed-Ahmad A. Investigating the effects of cysteine-118 oxidation on G12D KRas structure and dynamics: insights from MD simulations. J Biomol Struct Dyn 2024; 42:6968-6981. [PMID: 37480262 DOI: 10.1080/07391102.2023.2238080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Mutations of Ras proteins are believed to be among the most prominent causes of cancer. There is increasing evidence that the activity of Ras may be controlled by the redox state of cysteine residues located within the NKCD motif. This redox signaling is critical to both physiological and pathological processes and occurs when C118 is oxidized in a reversible manner. In this study, we used atomistic molecular dynamics simulations and Markov state models to investigate the structural and conformational effects of C118 oxidation on the oncogenic mutant KRas(G12D). While both mutants share common features and exhibit some distinct conformational states and fluctuations, we have found that the oxidized variant KRas(G12D/C118SOH) is more dynamic than the unoxidized counterpart, particularly in the switch II region. Additionally, C118 oxidation is found to alter the structure of the nucleotide-binding site and the switch regions as well as perturb the conformational equilibrium between Ras active and inactive states. These conformational preferences may alter the affinity to different effectors, resulting in selective downstream activation. Our results are anticipated to help future drug development efforts aimed at KRAS-related anticancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shimaa Salamh
- Department of Physics, Birzeit University, Birzeit, Palestine
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2
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Price BD, Sojka A, Maity S, Chavez IM, Starck M, Wilson MZ, Han S, Sherwin MS. Field-domain rapid-scan EPR at 240GHz for studies of protein functional dynamics at room temperature. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 366:107744. [PMID: 39096714 DOI: 10.1016/j.jmr.2024.107744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/05/2024]
Abstract
We present field-domain rapid-scan (RS) electron paramagnetic resonance (EPR) at 8.6T and 240GHz. To enable this technique, we upgraded a home-built EPR spectrometer with an FPGA-enabled digitizer and real-time processing software. The software leverages the Hilbert transform to recover the in-phase (I) and quadrature (Q) channels, and therefore the raw absorptive and dispersive signals, χ' and χ'', from their combined magnitude (I2+Q2). Averaging a magnitude is simpler than real-time coherent averaging and has the added benefit of permitting long-timescale signal averaging (up to at least 2.5×106 scans) because it eliminates the effects of source-receiver phase drift. Our rapid-scan (RS) EPR provides a signal-to-noise ratio that is approximately twice that of continuous wave (CW) EPR under the same experimental conditions, after scaling by the square root of acquisition time. We apply our RS EPR as an extension of the recently reported time-resolved Gd-Gd EPR (TiGGER) [Maity et al., 2023], which is able to monitor inter-residue distance changes during the photocycle of a photoresponsive protein through changes in the Gd-Gd dipolar couplings. RS, opposed to CW, returns field-swept spectra as a function of time with 10ms time resolution, and thus, adds a second dimension to the static field transients recorded by TiGGER. We were able to use RS TiGGER to track time-dependent and temperature-dependent kinetics of AsLOV2, a light-activated phototropin domain found in oats. The results presented here combine the benefits of RS EPR with the improved spectral resolution and sensitivity of Gd chelates at high magnetic fields. In the future, field-domain RS EPR at high magnetic fields may enable studies of other real-time kinetic processes with time resolutions that are otherwise difficult to access in the solution state.
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Affiliation(s)
- Brad D Price
- Department of Physics, University of California, Santa Barbara, 93106, CA, USA; Institute for Terahertz Science and Technology, University of California, Santa Barbara, 93106, CA, USA.
| | - Antonín Sojka
- Department of Physics, University of California, Santa Barbara, 93106, CA, USA; Institute for Terahertz Science and Technology, University of California, Santa Barbara, 93106, CA, USA
| | - Shiny Maity
- Department of Chemistry, University of California, Santa Barbara, 93106, CA, USA; Department of Chemistry, Northwestern University, 633 Clark Street, Evanston, 60208, IL, USA
| | - I Marcelo Chavez
- Department of Chemistry, University of California, Santa Barbara, 93106, CA, USA
| | - Matthieu Starck
- Department of Chemistry, Durham University, Durham, DH13LE, UK
| | - Maxwell Z Wilson
- Department Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, 93106, CA, USA
| | - Songi Han
- Department of Chemistry, University of California, Santa Barbara, 93106, CA, USA; Department of Chemistry, Northwestern University, 633 Clark Street, Evanston, 60208, IL, USA
| | - Mark S Sherwin
- Department of Physics, University of California, Santa Barbara, 93106, CA, USA; Institute for Terahertz Science and Technology, University of California, Santa Barbara, 93106, CA, USA.
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3
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Champion C, Lehner M, Smith AA, Ferrage F, Bolik-Coulon N, Riniker S. Unraveling motion in proteins by combining NMR relaxometry and molecular dynamics simulations: A case study on ubiquitin. J Chem Phys 2024; 160:104105. [PMID: 38465679 DOI: 10.1063/5.0188416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Nuclear magnetic resonance (NMR) relaxation experiments shine light onto the dynamics of molecular systems in the picosecond to millisecond timescales. As these methods cannot provide an atomically resolved view of the motion of atoms, functional groups, or domains giving rise to such signals, relaxation techniques have been combined with molecular dynamics (MD) simulations to obtain mechanistic descriptions and gain insights into the functional role of side chain or domain motion. In this work, we present a comparison of five computational methods that permit the joint analysis of MD simulations and NMR relaxation experiments. We discuss their relative strengths and areas of applicability and demonstrate how they may be utilized to interpret the dynamics in MD simulations with the small protein ubiquitin as a test system. We focus on the aliphatic side chains given the rigidity of the backbone of this protein. We find encouraging agreement between experiment, Markov state models built in the χ1/χ2 rotamer space of isoleucine residues, explicit rotamer jump models, and a decomposition of the motion using ROMANCE. These methods allow us to ascribe the dynamics to specific rotamer jumps. Simulations with eight different combinations of force field and water model highlight how the different metrics may be employed to pinpoint force field deficiencies. Furthermore, the presented comparison offers a perspective on the utility of NMR relaxation to serve as validation data for the prediction of kinetics by state-of-the-art biomolecular force fields.
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Affiliation(s)
- Candide Champion
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marc Lehner
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Albert A Smith
- Institute for Medical Physics and Biophysics, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Nicolas Bolik-Coulon
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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4
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Nencini R, Regnier MLG, Backlund SM, Mantzari E, Dunn CD, Ollila OHS. Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations. Commun Chem 2024; 7:28. [PMID: 38351219 PMCID: PMC10864328 DOI: 10.1038/s42004-024-01115-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not straightforward. Here we show that the dynamic landscape of peptide-containing molecular assemblies can be determined by a synergistic combination of solution state NMR experiments and molecular dynamics (MD) simulations. Solution state NMR experiments are straightforward to implement without an excessive amount of sample, while direct combination of spin relaxation data to MD simulations enables interpretation of dynamic landscapes of peptides and other aggregated molecules. To demonstrate this, we interpret NMR data from transmembrane, peripheral, and tail anchored peptides embedded in micelles. Our results indicate that peptides and detergent molecules do not rotate together as a rigid body, but peptides rotate in a viscous medium composed of detergent micelle. Spin relaxation times also provide indirect information on peptide conformational ensembles. This work gives new perspectives on peptide dynamics in complex biomolecular assemblies.
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Affiliation(s)
- Ricky Nencini
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | | | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Cory D Dunn
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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5
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Antila HS, Kav B, Miettinen MS, Martinez-Seara H, Jungwirth P, Ollila OHS. Emerging Era of Biomolecular Membrane Simulations: Automated Physically-Justified Force Field Development and Quality-Evaluated Databanks. J Phys Chem B 2022. [DOI: 10.1021/acs.jpcb.2c01954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne S. Antila
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum
Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
| | - Markus S. Miettinen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
- Department of Chemistry, University of Bergen, 5020 Bergen, Norway
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Biotechonology, University of Helsinki, Helsinki 00014, Finland
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6
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Valladares A, Oberoi G, Berg A, Beyer T, Unger E, Rausch I. Additively manufactured, solid object structures for adjustable image contrast in Magnetic Resonance Imaging. Z Med Phys 2022; 32:466-476. [PMID: 35597743 PMCID: PMC9948875 DOI: 10.1016/j.zemedi.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/08/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
The choice of materials challenges the development of Magnetic Resonance Imaging (MRI) phantoms and, to date, is mainly limited to water-filled compartments or gel-based components. Recently, solid materials have been introduced through additive manufacturing (AM) to mimic complex geometrical structures. Nonetheless, no such manufactured solid materials are available with controllable MRI contrast to mimic organ substructures or lesion heterogeneities. Here, we present a novel AM design that allows MRI contrast manipulation by varying the partial volume contribution to a ROI/voxel of MRI-visible material within an imaging object. Two sets of 11 cubes and three replicates of a spherical tumour model were designed and printed using AM. Most samples presented varying MRI-contrast in standard MRI sequences, based mainly on spin density and partial volume signal variation. A smooth and continuous MRI-contrast gradient could be generated in a single-compartment tumour model. This concept supports the development of more complex MRI phantoms that mimic the appearance of heterogeneous tumour tissues.
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Affiliation(s)
- Alejandra Valladares
- QIMP Team, Centre for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Gunpreet Oberoi
- Centre for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Andreas Berg
- Centre for Medical Physics and Biomedical Engineering, MR-Physics, Medical University of Vienna, Vienna, Austria,High-field MR-Center, Medical University of Vienna, Vienna, Austria
| | - Thomas Beyer
- QIMP Team, Centre for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Ewald Unger
- Centre for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Ivo Rausch
- QIMP Team, Centre for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria.
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7
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Tempra C, Ollila OHS, Javanainen M. Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension. J Chem Theory Comput 2022; 18:1862-1869. [PMID: 35133839 PMCID: PMC8908734 DOI: 10.1021/acs.jctc.1c00951] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lipid monolayers provide our lungs and eyes their functionality and serve as proxy systems in biomembrane research. Therefore, lipid monolayers have been studied intensively including using molecular dynamics simulations, which are able to probe their lateral structure and interactions with, e.g., pharmaceuticals or nanoparticles. However, such simulations have struggled in describing the forces at the air-water interface. Particularly, the surface tension of water and long-range van der Waals interactions have been considered critical, but their importance in monolayer simulations has been evaluated only separately. Here, we combine the recent C36/LJ-PME lipid force field that includes long-range van der Waals forces with water models that reproduce experimental surface tensions to elucidate the importance of these contributions in monolayer simulations. Our results suggest that a water model with correct surface tension is necessary to reproduce experimental surface pressure-area isotherms and monolayer phase behavior. The latter includes the liquid expanded and liquid condensed phases, their coexistence, and the opening of pores at the correct area per lipid upon expansion. Despite these improvements of the C36/LJ-PME with certain water models, the standard cutoff-based CHARMM36 lipid model with the 4-point OPC water model still provides the best agreement with experiments. Our results emphasize the importance of using high-quality water models in applications and parameter development in molecular dynamics simulations of biomolecules.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague 6, Czech Republic.,Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
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8
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Crawley T, Palmer AG. Bootstrap Aggregation for Model Selection in the Model-free Formalism. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:251-264. [PMID: 34414396 PMCID: PMC8372780 DOI: 10.5194/mr-2-251-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The ability to make robust inferences about the dynamics of biological macromolecules using NMR spectroscopy depends heavily on the application of appropriate theoretical models for nuclear spin relaxation. Data analysis for NMR laboratory-frame relaxation experiments typically involves selecting one of several model-free spectral density functions using a bias-corrected fitness test. Here, advances in statistical model selection theory, termed bootstrap aggregation or bagging, are applied to 15N spin relaxation data, developing a multimodel inference solution to the model-free selection problem. The approach is illustrated using data sets recorded at four static magnetic fields for the bZip domain of the S. cerevisiae transcription factor GCN4.
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Affiliation(s)
- Timothy Crawley
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
| | - Arthur G. Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, United States
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9
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Antila HS, M. Ferreira T, Ollila OHS, Miettinen MS. Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics. J Chem Inf Model 2021; 61:938-949. [PMID: 33496579 PMCID: PMC7903423 DOI: 10.1021/acs.jcim.0c01299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 01/08/2023]
Abstract
Molecular dynamics (MD) simulations are widely used to monitor time-resolved motions of biomacromolecules, although it often remains unknown how closely the conformational dynamics correspond to those occurring in real life. Here, we used a large set of open-access MD trajectories of phosphatidylcholine (PC) lipid bilayers to benchmark the conformational dynamics in several contemporary MD models (force fields) against nuclear magnetic resonance (NMR) data available in the literature: effective correlation times and spin-lattice relaxation rates. We found none of the tested MD models to fully reproduce the conformational dynamics. That said, the dynamics in CHARMM36 and Slipids are more realistic than in the Amber Lipid14, OPLS-based MacRog, and GROMOS-based Berger force fields, whose sampling of the glycerol backbone conformations is too slow. The performance of CHARMM36 persists when cholesterol is added to the bilayer, and when the hydration level is reduced. However, for conformational dynamics of the PC headgroup, both with and without cholesterol, Slipids provides the most realistic description because CHARMM36 overestimates the relative weight of ∼1 ns processes in the headgroup dynamics. We stress that not a single new simulation was run for the present work. This demonstrates the worth of open-access MD trajectory databanks for the indispensable step of any serious MD study: benchmarking the available force fields. We believe this proof of principle will inspire other novel applications of MD trajectory databanks and thus aid in developing biomolecular MD simulations into a true computational microscope-not only for lipid membranes but for all biomacromolecular systems.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Tiago M. Ferreira
- NMR
Group−Institute for Physics, Martin-Luther
University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | | | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
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10
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Virtanen SI, Kiirikki AM, Mikula KM, Iwaï H, Ollila OHS. Heterogeneous dynamics in partially disordered proteins. Phys Chem Chem Phys 2021; 22:21185-21196. [PMID: 32929427 DOI: 10.1039/d0cp03473h] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance of disordered protein regions is increasingly recognized in biology, but their characterization remains challenging due to the lack of suitable experimental and theoretical methods. NMR experiments can detect multiple timescale dynamics and structural details of disordered protein regions, but their detailed interpretation is often difficult. Here we combine protein backbone 15N spin relaxation data with molecular dynamics (MD) simulations to detect not only heterogeneous dynamics of large partially disordered proteins but also their conformational ensembles. We observed that the rotational dynamics of folded regions in partially disordered proteins is dominated by similar rigid body rotation as in globular proteins, thereby being largely independent of flexible disordered linkers. Disordered regions, on the other hand, exhibit complex rotational motions with multiple timescales below ∼30 ns which are difficult to detect from experimental data alone, but can be captured by MD simulations. Combining MD simulations and backbone 15N spin relaxation data, measured applying segmental isotopic labeling with salt-inducible split intein, we resolved the conformational ensemble and dynamics of partially disordered periplasmic domain of TonB protein from Helicobacter pylori containing 250 residues. To demonstrate the universality of our approach, it was applied also to the partially disordered region of chicken Engrailed 2. Our results pave the way in understanding how TonB transfers energy from inner membrane to the outer membrane receptors in Gram-negative bacteria, as well as the function of other proteins with disordered domains.
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Affiliation(s)
- Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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11
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Marcellini M, Nguyen MH, Martin M, Hologne M, Walker O. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. J Phys Chem B 2020; 124:5103-5112. [DOI: 10.1021/acs.jpcb.0c01922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Moreno Marcellini
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Minh-Ha Nguyen
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Marie Martin
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques (ISA), Univ Lyon, CNRS, UMR5280, Université Claude Bernard Lyon1, Lyon, France
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12
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Söderman O, Henriksson U. NMR Studies of Bicontinuous Liquid Crystalline Phases of Cubic Symmetry: Interpretation of Frequency-Dependent Relaxation Rates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5927-5934. [PMID: 32364742 DOI: 10.1021/acs.langmuir.0c00742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Extensive deuterium NMR relaxation data are presented for two specifically deuterium labeled surfactants forming bicontinuous cubic phases with water. 2H spin-lattice (R1) and spin-spin (R2) relaxation rates were measured over an extended frequency range from 2 to 60 MHz. The data are interpreted with an existing theoretical framework for spin relaxation in bicontinuous cubic phases, which takes its starting point in the description of bicontinuous phases using periodic minimal surfaces. We show that the theory succeeds in accounting for the data and that the defining parameters of the theory, correlation times and order parameters, are in agreement with related data in other surfactant phase situations. Specifically, we obtain the surfactant self-diffusion coefficient over the minimal surface in one unit cell and show that it is in agreement with the corresponding macroscopic NMR diffusion data. By measuring two additional NMR relaxation parameters for each carbon on the surfactant hydrocarbon tail, we demonstrate how order parameter and correlation time profiles can be obtained. Finally, we analyze published molecular dynamics trajectories for a bicontinuous cubic phase. The analysis provides further support for the theoretical framework used to interpret relaxation data.
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Affiliation(s)
- Olle Söderman
- Division of Physical Chemistry, Lund University, PO Box 124, SE-22100 Lund, Sweden
| | - Ulf Henriksson
- Division of Applied Physical Chemistry, Royal Institute of Technology, SE-10044 Stockholm, Sweden
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13
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Das S, Behera S, Balasubramanian S. Orientational Switch of the Lipase A Enzyme at the Oil-Water Interface: An Order of Magnitude Increase in Turnover Rate with a Single Surfactant Tag Explained. J Phys Chem Lett 2020; 11:2977-2982. [PMID: 32202805 DOI: 10.1021/acs.jpclett.0c00470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Interfacially active lipases can be immobilized at a biphasic interface to enhance turnover recyclability and to facilitate product separation. Extensive coarse-grained molecular dynamics simulations of lipase A (LipA) from Bacillus subtilis show a bimodal orientational distribution of the enzyme at an oil-water interface, arising from its ellipsoidal Janus particle-like character. The relative orientational preference can be tuned by pH. The simulations rationalize a rare experimental observation of an order of magnitude increase in the turnover rate of this lipase upon its noncovalent tagging by a single surfactant molecule at the interface, compared to its rate in bulk water. The adsorption free energy, the interfacial activation, a decrease in the number of orientational fluctuations, and an increased rate of translational diffusion, to all of which the Janus character of LipA contributes, are the factors responsible for this enhancement. This study can spur further investigations of the Janus behavior of enzymes to enhance their activity as well as to stabilize the biphasic emulsion needed for interfacial catalysis.
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Affiliation(s)
- Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sudarshan Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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14
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Javanainen M, Ollila OHS, Martinez-Seara H. Rotational Diffusion of Membrane Proteins in Crowded Membranes. J Phys Chem B 2020; 124:2994-3001. [PMID: 32188248 DOI: 10.1021/acs.jpcb.0c00884] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Membrane proteins travel along cellular membranes and reorient themselves to form functional oligomers and protein-lipid complexes. Following the Saffman-Delbrück model, protein radius sets the rate of this diffusive motion. However, it is unclear how this model, derived for ideal and dilute membranes, performs under crowded conditions of cellular membranes. Here, we study the rotational motion of membrane proteins using molecular dynamics simulations of coarse-grained membranes and 2-dimensional Lennard-Jones fluids with varying levels of crowding. We find that the Saffman-Delbrück model captures the size-dependency of rotational diffusion under dilute conditions where protein-protein interactions are negligible, whereas stronger scaling laws arise under crowding. Together with our recent work on lateral diffusion, our results reshape the description of protein dynamics in native membrane environments: The translational and rotational motions of proteins with small transmembrane domains are rapid, whereas larger proteins or protein complexes display substantially slower dynamics.
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Affiliation(s)
- Matti Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.,Computational Physics Laboratory, Tampere University, Tampere 33720, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic
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15
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Ciragan A, Backlund SM, Mikula KM, Beyer HM, Samuli Ollila OH, Iwaï H. NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein. Front Chem 2020; 8:136. [PMID: 32266203 PMCID: PMC7098700 DOI: 10.3389/fchem.2020.00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 11/22/2022] Open
Abstract
The growing understanding of partially unfolded proteins increasingly points to their biological relevance in allosteric regulation, complex formation, and protein design. However, the structural characterization of disordered proteins remains challenging. NMR methods can access both the dynamics and structures of such proteins, yet suffering from a high degeneracy of NMR signals. Here, we overcame this bottleneck utilizing a salt-inducible split intein to produce segmentally isotope-labeled samples with the native sequence, including the ligation junction. With this technique, we investigated the NMR structure and conformational dynamics of TonB from Helicobacter pylori in the presence of a proline-rich low complexity region. Spin relaxation experiments suggest that the several nano-second time scale dynamics of the C-terminal domain (CTD) is almost independent of the faster pico-to-nanosecond dynamics of the low complexity central region (LCCR). Our results demonstrate the utility of segmental isotopic labeling for proteins with heterogenous dynamics such as TonB and could advance NMR studies of other partially unfolded proteins.
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Affiliation(s)
- Annika Ciragan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Hoffmann F, Mulder FAA, Schäfer LV. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. J Chem Phys 2020; 152:084102. [DOI: 10.1063/1.5135379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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17
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Talley Edwards A, Javidialesaadi A, Weigandt KM, Stan G, Eads CD. Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13880-13892. [PMID: 31573205 PMCID: PMC10552554 DOI: 10.1021/acs.langmuir.9b01345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Predicting and controlling the properties of amphiphile aggregate mixtures require understanding the arrangements and dynamics of the constituent molecules. To explore these topics, we study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms to describe the dynamics. NMR relaxation rates, which depend on relative motions of interacting atom pairs, are influenced by wide distributions of dynamic time scales. We find that relative motions of neighboring atom pairs are rapid and liquidlike but are subject to structural constraints imposed by micelle morphology. Relative motions of distant atom pairs are slower than nearby atom pairs because changes in distances and angles are smaller when the moving atoms are further apart. Large numbers of atom pairs undergoing these slow relative motions contribute to predominantly negative cross-relaxation rates. For spherical micelles, but not for cylindrical micelles, cross-relaxation rates are positive only for surfactant tail atoms connected to the hydrophilic headgroup. This effect is related to the lower packing density of these atoms at the hydrophilic-hydrophobic boundary in spherical vs cylindrical arrangements, with correspondingly rapid and less constrained motion of atoms at the boundary.
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Affiliation(s)
- Allison Talley Edwards
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
- Corporate Research & Development, The Procter & Gamble Company, Mason, Ohio 45040, United States
| | | | - Katie M. Weigandt
- National Institute of Standards and Technology, 100 Bureau Drive, MS 6102, Gaithersburg, Maryland 20899, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Charles D. Eads
- Corporate Research & Development, The Procter & Gamble Company, Mason, Ohio 45040, United States
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18
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Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Rashid S, Lee BL, Wajda B, Spyracopoulos L. Side-Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations. J Phys Chem B 2019; 123:3665-3671. [PMID: 30973726 DOI: 10.1021/acs.jpcb.9b01741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
19F NMR spectroscopy is a powerful tool for the study of the structures, dynamics, and interactions of proteins bearing cysteine residues chemically modified with a trifluoroacetone group (CYF residue). 19F NMR relaxation rates for the fluoromethyl group of CYF residues are sensitive to overall rotational tumbling of proteins, fast rotation about the CF3 methyl axis, and the internal motion of the CYF side-chain. To develop a quantitative understanding of these various motional contributions, we used the model-free approach to extend expressions for 19F- T2 NMR relaxation to include side-chain motions for the CYF residue. We complemented the NMR studies with atomic views of methyl rotation and side-chain motions using molecular dynamics simulations. This combined methodology allows for quantitative separation of the contributions of fast pico- to nanosecond dynamics from micro- to millisecond exchange processes to the 19F line width and highlights the utility of the CYF residue as a sensitive reporter of side-chain environment and dynamics in proteins.
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Affiliation(s)
- Suad Rashid
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Brian L Lee
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Benjamin Wajda
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Leo Spyracopoulos
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
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20
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Oeemig JS, Ollila OS, Iwaï H. NMR structure of the C-terminal domain of TonB protein from Pseudomonas aeruginosa. PeerJ 2018; 6:e5412. [PMID: 30186676 PMCID: PMC6118199 DOI: 10.7717/peerj.5412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/19/2018] [Indexed: 11/20/2022] Open
Abstract
The TonB protein plays an essential role in the energy transduction system to drive active transport across the outer membrane (OM) using the proton-motive force of the cytoplasmic membrane of Gram-negative bacteria. The C-terminal domain (CTD) of TonB protein is known to interact with the conserved TonB box motif of TonB-dependent OM transporters, which likely induces structural changes in the OM transporters. Several distinct conformations of differently dissected CTDs of Escherichia coli TonB have been previously reported. Here we determined the solution NMR structure of a 96-residue fragment of Pseudomonas aeruginosa TonB (PaTonB-96). The structure shows a monomeric structure with the flexible C-terminal region (residues 338-342), different from the NMR structure of E. coli TonB (EcTonB-137). The extended and flexible C-terminal residues are confirmed by 15N relaxation analysis and molecular dynamics simulation. We created models for the PaTonB-96/TonB box interaction and propose that the internal fluctuations of PaTonB-96 makes it more accessible for the interactions with the TonB box and possibly plays a role in disrupting the plug domain of the TonB-dependent OM transporters.
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Affiliation(s)
- Jesper S. Oeemig
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- VIB Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel, Brussels, Belgium
| | - O.H. Samuli Ollila
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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21
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Hoffmann F, Xue M, Schäfer LV, Mulder FAA. Narrowing the gap between experimental and computational determination of methyl group dynamics in proteins. Phys Chem Chem Phys 2018; 20:24577-24590. [DOI: 10.1039/c8cp03915a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A synergistic analysis of methyl NMR relaxation data and MD simulations identifies ways to improve studies of protein dynamics.
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Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Mengjun Xue
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry
- University of Aarhus
- DK-8000 Aarhus
- Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry
- University of Aarhus
- DK-8000 Aarhus
- Denmark
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