1
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Steffen FD, Cunha RA, Sigel RKO, Börner R. FRET-guided modeling of nucleic acids. Nucleic Acids Res 2024; 52:e59. [PMID: 38869063 PMCID: PMC11260485 DOI: 10.1093/nar/gkae496] [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] [Received: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
The functional diversity of RNAs is encoded in their innate conformational heterogeneity. The combination of single-molecule spectroscopy and computational modeling offers new attractive opportunities to map structural transitions within nucleic acid ensembles. Here, we describe a framework to harmonize single-molecule Förster resonance energy transfer (FRET) measurements with molecular dynamics simulations and de novo structure prediction. Using either all-atom or implicit fluorophore modeling, we recreate FRET experiments in silico, visualize the underlying structural dynamics and quantify the reaction coordinates. Using multiple accessible-contact volumes as a post hoc scoring method for fragment assembly in Rosetta, we demonstrate that FRET can be used to filter a de novo RNA structure prediction ensemble by refuting models that are not compatible with in vitro FRET measurement. We benchmark our FRET-assisted modeling approach on double-labeled DNA strands and validate it against an intrinsically dynamic manganese(II)-binding riboswitch. We show that a FRET coordinate describing the assembly of a four-way junction allows our pipeline to recapitulate the global fold of the riboswitch displayed by the crystal structure. We conclude that computational fluorescence spectroscopy facilitates the interpretability of dynamic structural ensembles and improves the mechanistic understanding of nucleic acid interactions.
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Affiliation(s)
- Fabio D Steffen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard A Cunha
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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2
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Nüesch MF, Pietrek L, Holmstrom ED, Nettels D, von Roten V, Kronenberg-Tenga R, Medalia O, Hummer G, Schuler B. Nanosecond chain dynamics of single-stranded nucleic acids. Nat Commun 2024; 15:6010. [PMID: 39019880 PMCID: PMC11255343 DOI: 10.1038/s41467-024-50092-8] [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: 01/26/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and nanophotonic enhancement to determine the conformational ensembles and rapid chain dynamics of short single-stranded nucleic acids in solution. To interpret the experimental results in terms of end-to-end distance dynamics, we utilize the hierarchical chain growth approach, simple polymer models, and refinement with Bayesian inference to generate structural ensembles that closely align with the experimental data. The resulting chain reconfiguration times are exceedingly rapid, in the 10-ns range. Solvent viscosity-dependent measurements indicate that these dynamics of single-stranded nucleic acids exhibit negligible internal friction and are thus dominated by solvent friction. Our results provide a detailed view of the conformational distributions and rapid dynamics of single-stranded nucleic acids.
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Affiliation(s)
- Mark F Nüesch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lisa Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Erik D Holmstrom
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Valentin von Roten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rafael Kronenberg-Tenga
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany.
- Institute for Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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3
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Gauger M, Heinz M, Halbritter ALJ, Stelzl LS, Erlenbach N, Hummer G, Sigurdsson ST, Prisner TF. Structure and Internal Dynamics of Short RNA Duplexes Determined by a Combination of Pulsed EPR Methods and MD Simulations. Angew Chem Int Ed Engl 2024; 63:e202402498. [PMID: 38530284 DOI: 10.1002/anie.202402498] [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: 02/03/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20-base-pair-long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm- and singly fluorine-labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.
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Affiliation(s)
- Maximilian Gauger
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
| | - Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
| | | | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University, 55128, Mainz, Germany
- KOMET 1, Institute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128, Mainz, Germany
- Institute of Quantitative and Computational Bioscience (IQCB), Johannes Gutenberg University Mainz, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, 60438, Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 1, 60438, Frankfurt am Main, Germany
| | | | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Str. 7, 60438, Frankfurt am Main, Germany
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4
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Pietrek LM, Stelzl LS, Hummer G. Hierarchical Assembly of Single-Stranded RNA. J Chem Theory Comput 2024; 20:2246-2260. [PMID: 38361440 PMCID: PMC10938505 DOI: 10.1021/acs.jctc.3c01049] [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] [Received: 09/22/2023] [Revised: 12/09/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024]
Abstract
Single-stranded RNA (ssRNA) plays a major role in the flow of genetic information-most notably, in the form of messenger RNA (mRNA)-and in the regulation of biological processes. The highly dynamic nature of chains of unpaired nucleobases challenges structural characterizations of ssRNA by experiments or molecular dynamics (MD) simulations alike. Here, we use hierarchical chain growth (HCG) to construct ensembles of ssRNA chains. HCG assembles the structures of protein and nucleic acid chains from fragment libraries created by MD simulations. Applied to homo- and heteropolymeric ssRNAs of different lengths, we find that HCG produces structural ensembles that overall are in good agreement with diverse experiments, including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET). The agreement can be further improved by ensemble refinement using Bayesian inference of ensembles (BioEn). HCG can also be used to assemble RNA structures that combine base-paired and base-unpaired regions, as illustrated for the 5' untranslated region (UTR) of SARS-CoV-2 RNA.
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Affiliation(s)
- Lisa M. Pietrek
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Lukas S. Stelzl
- Faculty
of Biology, Johannes Gutenberg University
Mainz, Gresemundweg 2, 55128 Mainz, Germany
- KOMET
1, Institute of Physics, Johannes Gutenberg
University Mainz, 55099 Mainz, Germany
- Institute
of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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5
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Vedel IM, Papagiannoula A, Naudi-Fabra S, Milles S. Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems. Curr Opin Struct Biol 2023; 82:102659. [PMID: 37499445 PMCID: PMC10565672 DOI: 10.1016/j.sbi.2023.102659] [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] [Received: 03/03/2023] [Revised: 05/04/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. proteins without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence and nuclear magnetic resonance (NMR) spectroscopy are both exceptionally well suited to decipher and describe these states and their interconversion. Different time scales, from picoseconds to several milliseconds, can be addressed by both techniques. The length scales probed and the sample requirements (e.g. concentration, molecular weight, sample complexity) are, however, vastly different, making NMR and single molecule fluorescence an excellent combination for integrated studies. Here, we review recently undertaken approaches for the combined use of NMR and single molecule fluorescence to study protein dynamics.
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Affiliation(s)
- Ida Marie Vedel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Andromachi Papagiannoula
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Samuel Naudi-Fabra
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sigrid Milles
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany.
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6
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Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Curr Opin Struct Biol 2023; 78:102501. [PMID: 36463772 DOI: 10.1016/j.sbi.2022.102501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022]
Abstract
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here, we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. While atomistic molecular dynamics (MD) simulation has seen a lot of improvement in recent years, large-scale computing resources and careful validation are required to simulate full-length disordered biopolymers in solution. As a computationally efficient alternative, hierarchical chain growth (HCG) combines pre-sampled chain fragments in a statistically reproducible manner into ensembles of full-length atomically detailed biomolecular structures. Experimental data can be integrated during and after chain assembly. Applications to the neurodegeneration-linked proteins α-synuclein, tau, and TDP-43, including as condensate, illustrate the use of HCG. We conclude by highlighting the emerging connections to AI-based structural modeling including AlphaFold2.
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7
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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8
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Stelzl L, Pietrek LM, Holla A, Oroz J, Sikora M, Köfinger J, Schuler B, Zweckstetter M, Hummer G. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS AU 2022; 2:673-686. [PMID: 35373198 PMCID: PMC8970000 DOI: 10.1021/jacsau.1c00536] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 05/13/2023]
Abstract
The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure.
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Affiliation(s)
- Lukas
S. Stelzl
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Biology, Johannes Gutenberg University
Mainz, Gresemundweg 2, 55128 Mainz, Germany
- KOMET 1, Institute of Physics, Johannes
Gutenberg University Mainz, 55099 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Lisa M. Pietrek
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Andrea Holla
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Javier Oroz
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Rocasolano
Institute for Physical Chemistry, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mateusz Sikora
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, 8057 Zurich, Switzerland
| | - Markus Zweckstetter
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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9
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Muraru S, Muraru S, Nitu FR, Ionita M. Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods. J Chem Inf Model 2022; 62:232-239. [PMID: 35014791 DOI: 10.1021/acs.jcim.1c00957] [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] [Indexed: 12/14/2022]
Abstract
Computational methods can greatly aid nucleic acid fluorescence experiments by either offering fully detailed atomic insights into the conformations and interactions present in the studied system or by providing accurate simulations of the fundamental parameters. Fluorescence-based optical biosensors show great potential for clinical diagnosis of life-altering diseases with a very high specificity. Many of the designs for such rely on the concept of Förster resonance energy transfer (FRET). Currently, the methods used experimentally make use of theoretical assumptions which fundamentally affect the results. Having a detailed atomistic overview or significant simulated parameters could improve the understanding of the calculations and provide much more accurate outcomes. However, there are many challenges that need to be addressed before standardized computational protocols can be employed. This review is meant to highlight the progress made for computational methods used to simulate FRET experiments for nucleic acid probes. Recent advances have been made in computational tools, such as force field parametrizations and improved protocols. Complementary simulations to experimental data are also comprised in the this review.
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Affiliation(s)
- Sorin Muraru
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Sebastian Muraru
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Florentin Romeo Nitu
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
| | - Mariana Ionita
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania.,Advanced Polymer Materials Group, University Polithenica of Bucharest, Gh. Polizu Street 1-7, 011061 Bucharest, Romania
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10
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Grotz KK, Schwierz N. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D. J Chem Theory Comput 2022; 18:526-537. [PMID: 34881568 PMCID: PMC8757469 DOI: 10.1021/acs.jctc.1c00791] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Magnesium is essential in many vital processes. To correctly describe Mg2+ in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput. 2021, 17, 2530-2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg2+ parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg2+ force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 106 to 108 exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg2+, or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs.
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Affiliation(s)
- Kara K. Grotz
- Department of Theoretical
Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
| | - Nadine Schwierz
- Department of Theoretical
Biophysics, Max-Planck-Institute of Biophysics, Frankfurt am Main 60438, Germany
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11
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Klose D, Holla A, Gmeiner C, Nettels D, Ritsch I, Bross N, Yulikov M, Allain FHT, Schuler B, Jeschke G. Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries. Biophys J 2021; 120:4842-4858. [PMID: 34536387 PMCID: PMC8595751 DOI: 10.1016/j.bpj.2021.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/09/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
Förster resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) spectroscopy are complementary techniques for quantifying distances in the nanometer range. Both approaches are commonly employed for probing the conformations and conformational changes of biological macromolecules based on site-directed fluorescent or paramagnetic labeling. FRET can be applied in solution at ambient temperature and thus provides direct access to dynamics, especially if used at the single-molecule level, whereas EPR requires immobilization or work at cryogenic temperatures but provides data that can be more reliably used to extract distance distributions. However, a combined analysis of the complementary data from the two techniques has been complicated by the lack of a common modeling framework. Here, we demonstrate a systematic analysis approach based on rotamer libraries for both FRET and EPR labels to predict distance distributions between two labels from a structural model. Dynamics of the fluorophores within these distance distributions are taken into account by diffusional averaging, which improves the agreement with experiment. Benchmarking this methodology with a series of surface-exposed pairs of sites in a structured protein domain reveals that the lowest resolved distance differences can be as small as ∼0.25 nm for both techniques, with quantitative agreement between experimental and simulated transfer efficiencies within a range of ±0.045. Rotamer library analysis thus establishes a coherent way of treating experimental data from EPR and FRET and provides a basis for integrative structural modeling, including studies of conformational distributions and dynamics of biological macromolecules using both techniques.
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Affiliation(s)
- Daniel Klose
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Christoph Gmeiner
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Irina Ritsch
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nadja Bross
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Physics, University of Zurich, Zurich, Switzerland.
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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12
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Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays Biochem 2021; 65:37-49. [PMID: 33600559 PMCID: PMC8052285 DOI: 10.1042/ebc20200022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/17/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole-dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).
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Affiliation(s)
- Joshua C Sanders
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
| | - Erik D Holmstrom
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, U.S.A
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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Collauto A, Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Sören Bülow
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Dnyaneshwar B. Gophane
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Subham Saha
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Lukas S. Stelzl
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics Max Planck Institute of Biophysics Max-von-Laue-Str. 3 60438 Frankfurt am Main Germany
- Institute for Biophysics Goethe University Frankfurt Max-von-Laue-Str. 9 60438 Frankfurt am Main Germany
| | - Snorri T. Sigurdsson
- Department of Chemistry Science Institute University of Iceland Dunhagi 3 107 Reykjavík Iceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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15
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Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF. Compaction of RNA Duplexes in the Cell*. Angew Chem Int Ed Engl 2020; 59:23025-23029. [PMID: 32804430 PMCID: PMC7756485 DOI: 10.1002/anie.202009800] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/15/2022]
Abstract
The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus laevis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
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Affiliation(s)
- Alberto Collauto
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
| | - Sören von Bülow
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Dnyaneshwar B. Gophane
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Subham Saha
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Lukas S. Stelzl
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
| | - Gerhard Hummer
- Department of Theoretical BiophysicsMax Planck Institute of BiophysicsMax-von-Laue-Str. 360438Frankfurt am MainGermany
- Institute for BiophysicsGoethe University FrankfurtMax-von-Laue-Str. 960438Frankfurt am MainGermany
| | - Snorri T. Sigurdsson
- Department of ChemistryScience InstituteUniversity of IcelandDunhagi 3107ReykjavíkIceland
| | - Thomas F. Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Str. 760438Frankfurt am MainGermany
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16
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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17
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Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G. High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Res 2020; 48:924-933. [PMID: 31777925 PMCID: PMC6954412 DOI: 10.1093/nar/gkz1096] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/20/2019] [Indexed: 12/25/2022] Open
Abstract
Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.
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Affiliation(s)
- Marcel Heinz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Grace Thierolf
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nilesh R Kamble
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavk, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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18
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Pietrek LM, Stelzl LS, Hummer G. Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 16:725-737. [PMID: 31809054 DOI: 10.1021/acs.jctc.9b00809] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a large fraction of the human proteome and are critical in the regulation of cellular processes. A detailed understanding of the conformational dynamics of IDPs could help to elucidate their roles in health and disease. However, the inherent flexibility of IDPs makes structural studies and their interpretation challenging. Molecular dynamics (MD) simulations could address this challenge in principle, but inaccuracies in the simulation models and the need for long simulations have stymied progress. To overcome these limitations, we adopt a hierarchical approach that builds on the "flexible-meccano" model reported by Bernadó et al. (J. Am. Chem. Soc. 2005, 127, 17968-17969). First, we exhaustively sample small IDP fragments in all-atom simulations to capture their local structures. Then, we assemble the fragments into full-length IDPs to explore the stereochemically possible global structures of IDPs. The resulting ensembles of three-dimensional structures of full-length IDPs are highly diverse, much more so than in standard MD simulation. For the paradigmatic IDP α-synuclein, our ensemble captures both the local structure, as probed by nuclear magnetic resonance spectroscopy, and its overall dimension, as obtained from small-angle X-ray scattering in solution. By generating representative and meaningful starting ensembles, we can begin to exploit the massive parallelism afforded by current and future high-performance computing resources for atomic-resolution characterization of IDPs.
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Affiliation(s)
- Lisa M Pietrek
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany.,Institute for Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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19
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Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB, Schuler B. Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. Methods Enzymol 2018; 611:287-325. [PMID: 30471690 PMCID: PMC8018263 DOI: 10.1016/bs.mie.2018.09.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) sample structurally diverse ensembles. Characterizing the underlying distributions of conformations is a key step toward understanding the structural and functional properties of IDPs. One increasingly popular method for obtaining quantitative information on intramolecular distances and distributions is single-molecule Förster resonance energy transfer (FRET). Here we describe two essential elements of the quantitative analysis of single-molecule FRET data of IDPs: the sample-specific calibration of the single-molecule instrument that is required for determining accurate transfer efficiencies, and the use of state-of-the-art methods for inferring accurate distance distributions from these transfer efficiencies. First, we illustrate how to quantify the correction factors for instrument calibration with alternating donor and acceptor excitation measurements of labeled samples spanning a wide range of transfer efficiencies. Second, we show how to infer distance distributions based on suitably parameterized simple polymer models, and how to obtain conformational ensembles from Bayesian reweighting of molecular simulations or from parameter optimization in simplified coarse-grained models.
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Affiliation(s)
- Erik D Holmstrom
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Andrea Holla
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States.
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland; Department of Physics, University of Zurich, Zurich, Switzerland.
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