51
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Sun LZ, Zhang JX, Chen SJ. MCTBI: a web server for predicting metal ion effects in RNA structures. RNA (NEW YORK, N.Y.) 2017; 23:1155-1165. [PMID: 28450533 PMCID: PMC5513060 DOI: 10.1261/rna.060947.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/16/2017] [Indexed: 05/27/2023]
Abstract
Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Jing-Xiang Zhang
- School of Science and Technology, Zhejiang International Studies University, Hangzhou 310012, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, USA
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52
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Allred BE, Gebala M, Herschlag D. Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH +·C Wobble Formation in Double-Stranded DNA. J Am Chem Soc 2017; 139:7540-7548. [PMID: 28489947 PMCID: PMC5466006 DOI: 10.1021/jacs.7b01830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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The high charge density of nucleic
acids and resulting ion atmosphere
profoundly influence the conformational landscape of RNA and DNA and
their association with small molecules and proteins. Electrostatic
theories have been applied to quantitatively model the electrostatic
potential surrounding nucleic acids and the effects of the surrounding
ion atmosphere, but experimental measures of the potential and tests
of these models have often been complicated by conformational changes
and multisite binding equilibria, among other factors. We sought a
simple system to further test the basic predictions from electrostatics
theory and to measure the energetic consequences of the nucleic acid
electrostatic field. We turned to a DNA system developed by Bevilacqua
and co-workers that involves a proton as a ligand whose binding is
accompanied by formation of an internal AH+·C wobble
pair [Siegfried, N. A., et al. Biochemistry, 2010, 49, 3225]. Consistent with predictions
from polyelectrolyte models, we observed logarithmic dependences of
proton affinity versus salt concentration of −0.96 ± 0.03
and −0.52 ± 0.01 with monovalent and divalent cations,
respectively, and these results help clarify prior results that appeared
to conflict with these fundamental models. Strikingly, quantitation
of the ion atmosphere content indicates that divalent cations are
preferentially lost over monovalent cations upon A·C protonation,
providing experimental indication of the preferential localization
of more highly charged cations to the inner shell of the ion atmosphere.
The internal AH+·C wobble system further allowed us
to parse energetic contributions and extract estimates for the electrostatic
potential at the position of protonation. The results give a potential
near the DNA surface at 20 mM Mg2+ that is much less substantial
than at 20 mM K+ (−120 mV vs −210 mV). These
values and difference are similar to predictions from theory, and
the potential is substantially reduced at higher salt, also as predicted;
however, even at 1 M K+ the potential remains substantial,
counter to common assumptions. The A·C protonation module allows
extraction of new properties of the ion atmosphere and provides an
electrostatic meter that will allow local electrostatic potential
and energetics to be measured within nucleic acids and their complexes
with proteins.
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Affiliation(s)
- Benjamin E Allred
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States
| | - Magdalena Gebala
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States.,Department of Chemistry, Stanford University , Stanford, California 94305, United States.,ChEM-H Institute, Stanford University , Stanford, California 94305, United States
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53
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Abstract
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
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54
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Andrews CT, Campbell BA, Elcock AH. Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:1794-1811. [PMID: 28288277 DOI: 10.1021/acs.jctc.6b00883] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid side chains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of 20 amino acid side chain analogs interacting simultaneously with both a 70-base-pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid side chains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes. The estimated apparent free energies of interaction for ssDNA, on the other hand, correlate well with previous simulation values reported for interactions with isolated nucleobases, and with experimental values reported for interactions with guanosine. Comparisons of the interactions with dsDNA and ssDNA indicate that, with the exception of the positively charged side chains, all types of amino acid side chain interact more favorably with ssDNA, with intercalation of aromatic and aliphatic side chains being especially notable. Analysis of the data on a base-by-base basis indicates that positively charged side chains, as well as sodium ions, preferentially bind to cytosine in ssDNA, and that negatively charged side chains, and chloride ions, preferentially bind to guanine in ssDNA. These latter observations provide a novel explanation for the lower salt dependence of DNA duplex stability in GC-rich sequences relative to AT-rich sequences.
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Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Brady A Campbell
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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55
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Nguyen HT, Pabit SA, Pollack L, Case DA. Extracting water and ion distributions from solution x-ray scattering experiments. J Chem Phys 2017; 144:214105. [PMID: 27276943 DOI: 10.1063/1.4953037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Small-angle X-ray scattering measurements can provide valuable information about the solvent environment around biomolecules, but it can be difficult to extract solvent-specific information from observed intensity profiles. Intensities are proportional to the square of scattering amplitudes, which are complex quantities. Amplitudes in the forward direction are real, and the contribution from a solute of known structure (and from the waters it excludes) can be estimated from theory; hence, the amplitude arising from the solvent environment can be computed by difference. We have found that this "square root subtraction scheme" can be extended to non-zero q values, out to 0.1 Å(-1) for the systems considered here, since the phases arising from the solute and from the water environment are nearly identical in this angle range. This allows us to extract aspects of the water and ion distributions (beyond their total numbers), by combining experimental data for the complete system with calculations for the solutes. We use this approach to test molecular dynamics and integral-equation (3D-RISM (three-dimensional reference interaction site model)) models for solvent structure around myoglobin, lysozyme, and a 25 base-pair duplex DNA. Comparisons can be made both in Fourier space and in terms of the distribution of interatomic distances in real space. Generally, computed solvent distributions arising from the MD simulations fit experimental data better than those from 3D-RISM, even though the total small-angle X-ray scattering patterns are very similar; this illustrates the potential power of this sort of analysis to guide the development of computational models.
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Affiliation(s)
- Hung T Nguyen
- BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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56
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Gebala M, La Mantia F, Michaels PE, Ciampi S, Gupta B, Parker SG, Tavallaie R, Gooding JJ. Electric Field Modulation of Silicon upon Tethering of Highly Charged Nucleic Acids. Capacitive Studies on DNA‐modified Silicon (111). ELECTROANAL 2016. [DOI: 10.1002/elan.201600285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Magdalena Gebala
- Analytische Chemie – Elektroanalytik & Sensorik, Ruhr-Universität Bochum Universitätsstr.150 D-44780 Bochum Germany
- Department of Biochemistry Stanford University Stanford CA 94305 USA
| | - Fabio La Mantia
- Energiespeicher- und Energiewandlersysteme Universität Bremen Wiener Str. 12 D-28359 Bremen Germany
| | - Pauline Eugene Michaels
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Simone Ciampi
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Bakul Gupta
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Stephen G. Parker
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - Roya Tavallaie
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
| | - J. Justin Gooding
- School of Chemistry and the Australian Centre for NanoMedicine The University of New South Wales Sydney NSW 2052 Australia
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57
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Gebala M, Bonilla S, Bisaria N, Herschlag D. Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? J Am Chem Soc 2016; 138:10925-34. [PMID: 27479701 PMCID: PMC5010015 DOI: 10.1021/jacs.6b04289] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 01/14/2023]
Abstract
Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na(+) would outcompete Cs(+) by 1.8-2.1-fold; i.e., with Cs(+) in 2-fold excess of Na(+) the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res. 2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na(+) over Cs(+). There is an ∼25% preferential occupancy of Li(+) over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4-P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation-anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.
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Affiliation(s)
- Magdalena Gebala
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Steve Bonilla
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Namita Bisaria
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Daniel Herschlag
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
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58
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Jacobson DR, Saleh OA. Quantifying the ion atmosphere of unfolded, single-stranded nucleic acids using equilibrium dialysis and single-molecule methods. Nucleic Acids Res 2016; 44:3763-71. [PMID: 27036864 PMCID: PMC4856996 DOI: 10.1093/nar/gkw196] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
To form secondary structure, nucleic acids (NAs) must overcome electrostatic strand–strand repulsion, which is moderated by the surrounding atmosphere of screening ions. The free energy of NA folding therefore depends on the interactions of this ion atmosphere with both the folded and unfolded states. We quantify such interactions using the preferential ion interaction coefficient or ion excess: the number of ions present near the NA in excess of the bulk concentration. The ion excess of the folded, double-helical state has been extensively studied; however, much less is known about the salt-dependent ion excess of the unfolded, single-stranded state. We measure this quantity using three complementary approaches: a direct approach of Donnan equilibrium dialysis read out by atomic emission spectroscopy and two indirect approaches involving either single-molecule force spectroscopy or existing thermal denaturation data. The results of these three approaches, each involving an independent experimental technique, are in good agreement. Even though the single-stranded NAs are flexible polymers that are expected to adopt random-coil configurations, we find that their ion atmosphere is quantitatively described by rod-like models that neglect large-scale conformational freedom, an effect that we explain in terms of the competition between the relevant structural and electrostatic length scales.
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Affiliation(s)
- David R Jacobson
- Department of Physics, University of California, Santa Barbara, CA 93106, USA
| | - Omar A Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, CA, USA
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