1
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Toews S, Wacker A, Faison EM, Duchardt-Ferner E, Richter C, Mathieu D, Bottaro S, Zhang Q, Schwalbe H. The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH. Nucleic Acids Res 2024; 52:7971-7986. [PMID: 38842942 PMCID: PMC11260494 DOI: 10.1093/nar/gkae477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 07/23/2024] Open
Abstract
We present the nuclear magnetic resonance spectroscopy (NMR) solution structure of the 5'-terminal stem loop 5_SL1 (SL1) of the SARS-CoV-2 genome. SL1 contains two A-form helical elements and two regions with non-canonical structure, namely an apical pyrimidine-rich loop and an asymmetric internal loop with one and two nucleotides at the 5'- and 3'-terminal part of the sequence, respectively. The conformational ensemble representing the averaged solution structure of SL1 was validated using NMR residual dipolar coupling (RDC) and small-angle X-ray scattering (SAXS) data. We show that the internal loop is the major binding site for fragments of low molecular weight. This internal loop of SL1 can be stabilized by an A12-C28 interaction that promotes the transient formation of an A+•C base pair. As a consequence, the pKa of the internal loop adenosine A12 is shifted to 5.8, compared to a pKa of 3.63 of free adenosine. Furthermore, applying a recently developed pH-differential mutational profiling (PD-MaP) approach, we not only recapitulated our NMR findings of SL1 but also unveiled multiple sites potentially sensitive to pH across the 5'-UTR of SARS-CoV-2.
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Affiliation(s)
- Sabrina Toews
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Edgar M Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - Elke Duchardt-Ferner
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
| | - Daniel Mathieu
- Bruker BioSpin GmbH, Ettlingen, Baden-Württemberg 76275, Germany
| | - Sandro Bottaro
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/Main, Hesse 60438, Germany
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2
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Cardoso S, Sousa F, Pessoa Filho PA, R Azzoni A. Understanding the adsorption of plasmid DNA and RNA molecules onto arginine-agarose chromatographic resin. Mol Biol Rep 2022; 49:3893-3901. [PMID: 35178684 PMCID: PMC8853897 DOI: 10.1007/s11033-022-07239-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
Background The production of nucleic acids (plasmid DNA or mRNA) in response to the development of new advanced vaccine platforms has greatly increased recently, mostly resulting from the pandemic situation. Due to the intended pharmaceutical use, nucleic acids preparations must fulfill all the required specifications in terms of purity and quality. Chromatography is a standard operation used to isolate these molecules from impurities, playing a central role in the manufacturing processes. However, the mechanism of nucleic acid adsorption in chromatographic resins is poorly understood, often leading to low adsorption capacities and a lack of specificity. Methods and results Here we investigated the adsorption of plasmid DNA and RNA molecules onto arginine-agarose, a resin with potential for large-scale application. Equilibrium batch studies were performed through pre-purified samples, using arginine-based ligands by varying the adsorption conditions in the pH value range from 6.0 to 9.0. Langmuir and Freundlich isotherm models were used to describe the adsorption equilibrium. The best fit for both nucleic acids was achieved using the Freundlich model. The correct choice of pH showed critical for controlling the efficacy of arginine-nucleic acid interaction, due to its influence on the nucleic acid structures. This type of analysis is necessary for the improvement of the selectivity and binding capacities of the resins used for plasmid DNA or mRNA purification. Conclusions The results presented here indicate that adsorption conditions can be tuned to enhance separation between pDNA and RNA, an important feature in the purification of nucleic acids for vaccine production.
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Affiliation(s)
- Sara Cardoso
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil
| | - Fani Sousa
- CICS-UBI - Centro de Investigação de Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506, Covilhã, Portugal
| | - Pedro A Pessoa Filho
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil
| | - Adriano R Azzoni
- Departamento de Engenharia Química, Escola Politécnica da Universidade de São Paulo, Av. Prof. Luciano Gualberto, Trav. 3, Nº 380, São Paulo, SP, CEP 05508-900, Brazil.
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3
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Huai Z, Sun Z. Titration of Adenine in a GA Mismatch with Grand Canonical Simulations. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2020. [DOI: 10.1142/s2737416520420053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Computational prediction of the pKa of ionizable groups remains a central challenge in biomolecular modeling. Although all-atom fixed-charge force fields could be accurate to describe the interaction network within the biomolecules, proper sampling techniques are required to obtain the thermodynamic information in the (de)protonation event. Sufficient sampling requires an ensemble of structures from simulations with proper treatments of the acid-base equilibria, and the grand canonical simulation technique could be used to model the growth/annihilation of hydrogen atoms by merging Hamiltonians of different protonation states into one simulation ensemble. The electrostatic feature of nucleotide systems is especially difficult to model, and the situation becomes more challenging when the ionizable site is highly perturbed. Although there are many successful predictions obtained from the grand canonical constant pH simulations, few reports focus on highly perturbed nucleotide systems with unconventional base-pair features. In this work, with the discrete constant pH method, we investigate the titration thermodynamics of an adenine in the catalytic triad in a 35-nucleotide single-stranded RNA hairpin, featuring an unconventional GA mismatch and a substantially shifted pKa value. Validation tests are performed with two system setups, both of which provide pKa predictions in good agreement with the experimental value. A single-configuration-based technique is used to calculate the pKa for comparison. The current success indicates the predictive power of the current nucleotide modeling framework.
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Affiliation(s)
- Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
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4
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Paul TJ, Vilseck JZ, Hayes RL, Brooks CL. Exploring pH Dependent Host/Guest Binding Affinities. J Phys Chem B 2020; 124:6520-6528. [PMID: 32628482 DOI: 10.1021/acs.jpcb.0c03671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm. In the present paper, we apply a simple two-step approach to calculate the pH-dependent binding free energy of a model cucubit[7]uril host/guest system. By use of λ-dynamics with an enhanced sampling protocol, adaptive landscape flattening, pKa shifts and reference binding free energies upon complexation were determined. This information enables the construction of pH-dependent binding profiles that accurately capture the pKa shifts and reproduce binding free energies at the different pH conditions that were observed experimentally. Our calculations illustrate a general framework for computing pH-dependent binding free energies but also point to some issues in modeling the molecular charge distributions within this series of molecules with CGenFF. However, by introducing some minor charge modifications to the CGenFF force field, we saw significant improvement in accuracy of the calculated pKa shifts.
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5
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M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. Proc Natl Acad Sci U S A 2020; 117:3583-3591. [PMID: 32015120 DOI: 10.1073/pnas.1913385117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The matrix-2 (M2) protein from influenza A virus is a tetrameric, integral transmembrane (TM) protein that plays a vital role in viral replication by proton flux into the virus. The His37 tetrad is a pH sensor in the center of the M2 TM helix that activates the channel in response to the low endosomal pH. M2 consists of different regions that are believed to be involved in membrane targeting, packaging, nucleocapsid binding, and proton transport. Although M2 has been the target of many experimental and theoretical studies that have led to significant insights into its structure and function under differing conditions, the main mechanism of proton transport, its conformational dynamics, and the role of the amphipathic helices (AHs) on proton conductance remain elusive. To this end, we have applied explicit solvent constant pH molecular dynamics using the multisite λ-dynamics approach (CpHMDMSλD) to investigate the buried ionizable residues comprehensively and to elucidate their effect on the conformational transition. Our model recapitulates the pH-dependent conformational transition of M2 from closed to open state when the AH domain is included in the M2 construct, revealing the role of the amphipathic helices on this transition and shedding light on the proton-transport mechanism. This work demonstrates the importance of including the amphipathic helices in future experimental and theoretical studies of ion channels. Finally, our work shows that explicit solvent CpHMDMSλD provides a realistic pH-dependent model for membrane proteins.
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6
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Cheng R, Loire E, Martens J, Fridgen TD. An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase. Phys Chem Chem Phys 2020; 22:2999-3007. [DOI: 10.1039/c9cp06393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.
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Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO
- Campus Universite d’Orsay
- France
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Nijmegen
- The Netherlands
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7
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Pasquali S, Frezza E, Barroso da Silva FL. Coarse-grained dynamic RNA titration simulations. Interface Focus 2019; 9:20180066. [PMID: 31065339 DOI: 10.1098/rsfs.2018.0066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule's structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local pK a values for each nucleotide.
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Affiliation(s)
- S Pasquali
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Université Paris Descartes, Paris 75006, France
| | - E Frezza
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Université Paris Descartes, Paris 75006, France
| | - F L Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciência s Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/no, Ribeirão Preto, SP BR-14040-903, Brazil.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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8
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Halder A, Vemuri S, Roy R, Katuri J, Bhattacharyya D, Mitra A. Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function. ACS OMEGA 2019; 4:699-709. [PMID: 30775644 PMCID: PMC6372247 DOI: 10.1021/acsomega.8b02908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/25/2018] [Indexed: 05/05/2023]
Abstract
Charged nucleobases have been found to occur in several known RNA molecules and are considered essential for their structure and function. The mechanism of their involvement is however not yet fully understood. Revelation of the role of N7-protonated guanine, in modulating the geometry and stability of noncanonical base pairs formed through its unprotonated edges [Watson-Crick (WC) and sugar], has triggered the need to evaluate the feasibility of similar roles of other protonated nucleobases [Halder et al., Phys Chem Chem Phys, 2015, 17, 26249]. In this context, N3 protonation of guanine makes an interesting case as its influence on the charge distribution of the WC edge is similar to that of N7 protonation, though its thermodynamic cost of protonation is significantly higher. In this work, we have carried out structural bioinformatics analyses and quantum mechanics-based calculations to show that N3 protonation of guanine may take place in a cellular environment, at least in the G:C W:W Trans and G:G W:H Cis base pairs. Our results provide a reasonable starting point for future investigations in order to address the larger mechanistic question.
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Affiliation(s)
- Antarip Halder
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Saurabh Vemuri
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Rohit Roy
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Jayanth Katuri
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Dhananjay Bhattacharyya
- Computational
Science Division, Saha Institute of Nuclear
Physics (SINP), 1/AF,
Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
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9
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Cardoso S, de Alcântara Pessoa Filho P, Sousa F, Rodrigues Azzoni A. Arginine and di-arginine ligands for plasmid DNA purification using negative chromatography. Sep Purif Technol 2018. [DOI: 10.1016/j.seppur.2018.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018; 140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A wobble A·C pair can be protonated at near physiological pH to form a more stable wobble A+·C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A·C mismatch on the top (near the loop, U22C), middle (U25C), and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A·C pair substitution and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of an apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (∼2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (∼1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.
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Affiliation(s)
- Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,School of Physics, and State Key Laboratory of Optoelectronic Materials and Technologies , Sun Yat-sen University , Guangzhou 510275 , People's Republic of China
| | - Cailing Tong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yiran Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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11
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Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 2017; 13:5933-5944. [PMID: 29111720 DOI: 10.1021/acs.jctc.7b00875] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementation of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.
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Affiliation(s)
- Brian K Radak
- Leadership Computing Facility, Argonne National Laboratory , Argonne, Illinois 60439-8643, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine, Université de Lorraine , B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France.,Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2325, United States
| | - Donghyuk Suh
- Department of Chemistry, University of Chicago , Chicago, Illinois 60637-1454, United States
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory , Argonne, Illinois 60439-8643, United States
| | - Wei Jiang
- Leadership Computing Facility, Argonne National Laboratory , Argonne, Illinois 60439-8643, United States
| | - James C Phillips
- Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2325, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2325, United States.,Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-2325, United States
| | - Benoît Roux
- Department of Chemistry, University of Chicago , Chicago, Illinois 60637-1454, United States.,Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637-1454, United States.,Center for Nanoscale Materials, Argonne National Laboratory , Argonne, Illinois 60439-8643, United States
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12
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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13
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Barroso da Silva FL, Derreumaux P, Pasquali S. Fast coarse-grained model for RNA titration. J Chem Phys 2017; 146:035101. [PMID: 28109220 DOI: 10.1063/1.4972986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.
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Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ave. do café, s/no, BR-14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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14
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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15
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Synthesis of two 6-aza-uridines modified by benzoheterocycle as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.05.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, Im W. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem 2017; 38:1114-1124. [PMID: 27862047 PMCID: PMC5403596 DOI: 10.1002/jcc.24660] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, 9700 Cass Ave, Argonne, Illinois
| | - Xi Cheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Jumin Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Seonghoon Kim
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Sang-Jun Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Dhilon S Patel
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Andrew H Beaven
- Department of Chemistry, The University of Kansas, Lawrence, Kansas
| | - Kyu Il Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Huan Rui
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Soohyung Park
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Hui Sun Lee
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Jeffrey B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, University of Maryland College Park, Maryland
| | - Yifei Qi
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
| | - Wonpil Im
- Department of Biological Sciences and Bioengineering Program, Lehigh University, Pennsylvania
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17
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Barroso da Silva FL, MacKernan D. Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations. J Chem Theory Comput 2017; 13:2915-2929. [DOI: 10.1021/acs.jctc.6b01114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento
de Fı́sica e Quı́mica, Faculdade
de Ciências Farmacêuticas de Ribeirão Preto,
Av. do café, s/no. − Universidade de São Paulo, BR-14040-903 Ribeirão Preto, São Paulo, Brazil
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18
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Bui MN, Brittany Johnson M, Viard M, Satterwhite E, Martins AN, Li Z, Marriott I, Afonin KA, Khisamutdinov EF. Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2017; 13:1137-1146. [PMID: 28064006 PMCID: PMC6637421 DOI: 10.1016/j.nano.2016.12.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/21/2022]
Abstract
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles. The tetra-U RNA motif was implemented to construct four functional triangles using RNA, DNA and RNA/DNA mixtures, resulting in fine-tunable enzymatic and thermodynamic stabilities, immunostimulatory activity and RNAi capability. Moreover, the tetra-U toolkit has great potential in the fabrication of rectangular, pentagonal, and hexagonal NPs, representing the power of simplicity of RNA/DNA approach for RNA nanotechnology and nanomedicine community.
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Affiliation(s)
- My N Bui
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Emily Satterwhite
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
| | - Angelica N Martins
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Ian Marriott
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
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19
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Bodnarchuk MS, Doncom KEB, Wright DB, Heyes DM, Dini D, O'Reilly RK. Polyelectrolyte pKa from experiment and molecular dynamics simulation. RSC Adv 2017. [DOI: 10.1039/c6ra27785c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pKa of a polyelectrolyte has been determined experimentally by potentiometric titration and computed using Molecular Dynamics (MD) constant pH (CpH) methodology, which allows the pKa of each titratable site along the polymer backbone.
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Affiliation(s)
| | | | | | - David M. Heyes
- Department of Mechanical Engineering
- Imperial College
- London SW7 2AZ
- UK
| | - Daniele Dini
- Department of Mechanical Engineering
- Imperial College
- London SW7 2AZ
- UK
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20
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Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 2016; 12:5411-5421. [PMID: 27709966 DOI: 10.1021/acs.jctc.6b00552] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.
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Affiliation(s)
- Yandong Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Wei Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Jason A Wallace
- University of Oklahoma College of Dentistry , Oklahoma City, Oklahoma 73117, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
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21
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Chen Y, Roux B. Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method. J Chem Theory Comput 2016; 11:3919-31. [PMID: 26300709 PMCID: PMC4535364 DOI: 10.1021/acs.jctc.5b00261] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern (J. Chem. Phys. 2007, 126, 164112), consists of carrying out short nonequilibrium molecular dynamics (neMD) switching trajectories to generate physically plausible configurations with changed protonation states that are subsequently accepted or rejected according to a Metropolis Monte Carlo (MC) criterion. To ensure microscopic detailed balance arising from such nonequilibrium switches, the atomic momenta are altered according to the symmetric two-ends momentum reversal prescription. To achieve higher efficiency, the original neMD-MC scheme is separated into two steps, reducing the need for generating a large number of unproductive and costly nonequilibrium trajectories. In the first step, the protonation state of a site is randomly attributed via a Metropolis MC process on the basis of an intrinsic pKa; an attempted nonequilibrium switch is generated only if this change in protonation state is accepted. This hybrid two-step inherent pKa neMD-MC simulation method is tested with single amino acids in solution (Asp, Glu, and His) and then applied to turkey ovomucoid third domain and hen egg-white lysozyme. Because of the simple linear increase in the computational cost relative to the number of titratable sites, the present method is naturally able to treat extremely large systems.
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Affiliation(s)
- Yunjie Chen
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago , Chicago, Illinois 60637, United States
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22
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Wu RR, Yang B, Frieler CE, Berden G, Oomens J, Rodgers MT. Diverse mixtures of 2,4-dihydroxy tautomers and O4 protonated conformers of uridine and 2'-deoxyuridine coexist in the gas phase. Phys Chem Chem Phys 2016. [PMID: 26225730 DOI: 10.1039/c5cp02227d] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The gas-phase conformations of protonated uridine, [Urd+H](+), and its modified form, protonated 2'-deoxyuridine, [dUrd+H](+), generated by electrospray ionization are investigated using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques. IRMPD action spectra of [Urd+H](+) and [dUrd+H](+) are measured over the IR fingerprint and hydrogen-stretching regions. [Urd+H](+) and [dUrd+H](+) exhibit very similar IRMPD spectral profiles. However, the IRMPD yields of [Urd+H](+) exceed those of [dUrd+H](+) in both the IR fingerprint and hydrogen-stretching regions. The measured spectra are compared to the linear IR spectra predicted for the stable low-energy structures of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the tautomeric conformations populated by electrospray ionization. Both B3LYP and MP2 methods find O4 and O2 protonated canonical as well as 2,4-dihydroxy tautomers among the stable low-energy structures of [Urd+H](+) and [dUrd+H](+). Comparison between the measured IRMPD and calculated linear IR spectra suggests that these species exist in their ring-closed forms and that both 2,4-dihydroxy tautomers as well as O4 protonated canonical conformers coexist in the population generated by electrospray ionization for both [Urd+H](+) and [dUrd+H](+). The 2'-deoxy modification of [dUrd+H](+) reduces the variety of 2,4-dihydroxy tautomers populated in the experiments vs. those of [Urd+H](+).
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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23
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Coarse-grained modeling of RNA 3D structure. Methods 2016; 103:138-56. [PMID: 27125734 DOI: 10.1016/j.ymeth.2016.04.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022] Open
Abstract
Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.
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24
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Gaines CS, York DM. Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation. J Am Chem Soc 2016; 138:3058-65. [PMID: 26859432 PMCID: PMC4904722 DOI: 10.1021/jacs.5b12061] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present results from molecular dynamics simulations and free energy calculations of the twister ribozyme at different stages along the reaction path to gain insight into its mechanism. The results, together with recent biochemical experiments, provide support for a mechanism involving general-acid catalysis by a conserved adenine residue in the active site. Although adenine has been previously implicated as a general acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be a twist. Biochemical experiments suggest that general acid catalysis may occur through the N3 position, which has never before been implicated in this role; however, currently, there is a lack of a detailed structural model for the active state of the twister ribozyme in solution that is consistent with these and other experiments. Simulations in a crystalline environment reported here are consistent with X-ray crystallographic data, and suggest that crystal packing contacts trap the RNA in an inactive conformation with U-1 in an extruded state that is incompatible with an in-line attack to the scissile phosphate. Simulations in solution, on the other hand, reveal this region to be dynamic and able to adopt a conformation where U-1 is stacked with G33. In this state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 position of A1 are poised to act as a general base and acid, respectively, as supported by mutational experiments. Free energy calculations further predict the electrostatic environment causes a shift of the microscopic pKa at the N3 position of A1 toward neutrality by approximately 5 pKa units. These results offer a unified interpretation of a broad range of currently available experimental data that points to a novel mode of general acid catalysis through the N3 position of an adenine nucleobase, thus expanding the repertoire of known mechanistic strategies employed by small nucleolytic ribozymes.
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Affiliation(s)
- Colin S. Gaines
- Center for Integrative Proteomics Research and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
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25
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Abstract
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002 CNRS/Université de Strasbourg, 15, rue René Descartes, Strasbourg Cedex, 67084, France
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26
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Kim MO, McCammon JA. Computation of pH-dependent binding free energies. Biopolymers 2016; 105:43-9. [PMID: 26202905 PMCID: PMC4623928 DOI: 10.1002/bip.22702] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 07/20/2015] [Indexed: 01/21/2023]
Abstract
Protein-ligand binding accompanies changes in the surrounding electrostatic environments of the two binding partners and may lead to changes in protonation upon binding. In cases where the complex formation results in a net transfer of protons, the binding process is pH-dependent. However, conventional free energy computations or molecular docking protocols typically employ fixed protonation states for the titratable groups in both binding partners set a priori, which are identical for the free and bound states. In this review, we draw attention to these important yet largely ignored binding-induced protonation changes in protein-ligand association by outlining physical origins and prevalence of the protonation changes upon binding. Following a summary of various theoretical methods for pKa prediction, we discuss the theoretical framework to examine the pH dependence of protein-ligand binding processes.
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Affiliation(s)
- M. Olivia Kim
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - J. Andrew McCammon
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
- National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, USA
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27
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Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol 2015; 11:e1004341. [PMID: 26506513 PMCID: PMC4623973 DOI: 10.1371/journal.pcbi.1004341] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/17/2015] [Indexed: 11/19/2022] Open
Abstract
BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD) framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems. Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease, a devastating neurodegenerative disorder causing dementia. Site-specific hydrolytic catalysis of β-secretase, or BACE-1, is responsible for production of oligomerative amyloid β-peptide. As the catalytic activity of BACE-1 is pH-dependent and its structural dynamics are intrinsic to the catalysis, we examine the dependence of dynamics of BACE-1 on solution pH and its implications on the catalytic mechanism of BACE-1. Also, we highlight the importance of accurate description of protonation states of the titratable groups in computer-aided drug discovery targeting BACE-1. We hope the understanding of pH dependence of the dynamics and inhibitor binding properties of BACE-1 will aid the structure-based inhibitor design efforts against Alzheimer’s disease.
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28
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Goh GB, Eike DM, Murch BP, Brooks CL. Accurate Modeling of Ionic Surfactants at High Concentration. J Phys Chem B 2015; 119:6217-24. [DOI: 10.1021/acs.jpcb.5b01765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Garrett B. Goh
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - David M. Eike
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Bruce P. Murch
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
- Biophysics
Program, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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29
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Abstract
![]()
In
this work, we apply the recently developed constant pH molecular
dynamics technique to study protonation equilibria of titratable side
chains in the context of simple transmembrane (TM) helices and explore
the effect of pH on their configurations in membrane bilayers. We
observe that, despite a significant shift toward neutral states, considerable
population of different side chains stay in the charged state that
give rise to pKa values around 9.6 for
Asp and Glu and 4.5 to 6 for His and Lys side chains, respectively.
These charged states are highly stabilized by favorable interactions
between head groups, water molecules, and the charged side chains
that are facilitated by substantial changes in the configuration of
the peptides. The pH dependent configurations and the measured pKa values are in good agreement with relatively
recent solid state NMR measurements. Our results presented here demonstrate
that all-atom constant pH molecular dynamics can be applied to membrane
proteins and peptides to obtain reliable pKa values and pH dependent behavior for these systems.
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Affiliation(s)
- Afra Panahi
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
| | - Charles L Brooks
- †Department of Chemistry and ‡Biophysics Program, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan, 48109, United States
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30
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Laricheva EN, Goh GB, Dickson A, Brooks CL. pH-dependent transient conformational states control optical properties in cyan fluorescent protein. J Am Chem Soc 2015; 137:2892-900. [PMID: 25647152 PMCID: PMC4394632 DOI: 10.1021/ja509233r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently engineered mutant of cyan fluorescent protein (WasCFP) that exhibits pH-dependent absorption suggests that its tryptophan-based chromophore switches between neutral (protonated) and charged (deprotonated) states depending on external pH. At pH 8.1, the latter gives rise to green fluorescence as opposed to the cyan color of emission that is characteristic for the neutral form at low pH. Given the high energy cost of deprotonating the tryptophan at the indole nitrogen, this behavior is puzzling, even if the stabilizing effect of the V61K mutation in proximity to the protonation/deprotonation site is considered. Because of its potential to open new avenues for the development of optical sensors and photoconvertible fluorescent proteins, a mechanistic understanding of how the charged state in WasCFP can possibly be stabilized is thus important. Attributed to the dynamic nature of proteins, such understanding often requires knowledge of the various conformations adopted, including transiently populated conformational states. Transient conformational states triggered by pH are of emerging interest and have been shown to be important whenever ionizable groups interact with hydrophobic environments. Using a combination of the weighted-ensemble sampling method and explicit-solvent constant pH molecular dynamics (CPHMD(MSλD)) simulations, we have identified a solvated transient state, characterized by a partially open β-barrel where the chromophore pKa of 6.8 is shifted by over 20 units from that of the closed form (6.8 and 31.7, respectively). This state contributes a small population at low pH (12% at pH 6.1) but becomes dominant at mildly basic conditions, contributing as much as 53% at pH 8.1. This pH-dependent population shift between neutral (at pH 6.1) and charged (at pH 8.1) forms is thus responsible for the observed absorption behavior of WasCFP. Our findings demonstrate the conditions necessary to stabilize the charged state of the WasCFP chromophore (namely, local solvation at the deprotonation site and a partial flexibility of the protein β-barrel structure) and provide the first evidence that transient conformational states can control optical properties of fluorescent proteins.
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Affiliation(s)
- Elena N. Laricheva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Garrett B. Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alex Dickson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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31
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Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry 2015; 54:1307-13. [PMID: 25615525 DOI: 10.1021/bi5012833] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.
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Affiliation(s)
- Thakshila Dissanayake
- Center for Integrative Proteomics Research, BioMaPS Institute, and Department of Chemistry & Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States
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32
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Zhang S, Ganguly A, Goyal P, Bingaman J, Bevilacqua PC, Hammes-Schiffer S. Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. J Am Chem Soc 2015; 137:784-98. [PMID: 25526516 PMCID: PMC4308743 DOI: 10.1021/ja510387y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/30/2022]
Abstract
The glmS ribozyme catalyzes a self-cleavage reaction at the phosphodiester bond between residues A-1 and G1. This reaction is thought to occur by an acid-base mechanism involving the glucosamine-6-phosphate cofactor and G40 residue. Herein quantum mechanical/molecular mechanical free energy simulations and pKa calculations, as well as experimental measurements of the rate constant for self-cleavage, are utilized to elucidate the mechanism, particularly the role of G40. Our calculations suggest that an external base deprotonates either G40(N1) or possibly A-1(O2'), which would be followed by proton transfer from G40(N1) to A-1(O2'). After this initial deprotonation, A-1(O2') starts attacking the phosphate as a hydroxyl group, which is hydrogen-bonded to deprotonated G40, concurrent with G40(N1) moving closer to the hydroxyl group and directing the in-line attack. Proton transfer from A-1(O2') to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cleavage reaction. A mechanism in which an external base does not participate, but rather the proton transfers from A-1(O2') to a nonbridging oxygen during nucleophilic attack, was also considered but deemed to be less likely due to its higher effective free energy barrier. The calculated rate constant for the favored mechanism is in agreement with the experimental rate constant measured at biological Mg(2+) ion concentration. According to these calculations, catalysis is optimal when G40 has an elevated pKa rather than a pKa shifted toward neutrality, although a balance among the pKa's of A-1, G40, and the nonbridging oxygen is essential. These results have general implications, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40.
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Affiliation(s)
- Sixue Zhang
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Abir Ganguly
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Puja Goyal
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jamie
L. Bingaman
- Department
of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department
of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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33
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Bergonzo C, Galindo-Murillo R, Cheatham TE. Molecular modeling of nucleic Acid structure: electrostatics and solvation. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 55:7.9.1-27. [PMID: 25631536 DOI: 10.1002/0471142700.nc0709s55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit.
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Affiliation(s)
- Christina Bergonzo
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah
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34
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Chen W, Shen JK. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics. J Comput Chem 2014; 35:1986-96. [PMID: 25142416 PMCID: PMC4165709 DOI: 10.1002/jcc.23713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/20/2014] [Accepted: 08/03/2014] [Indexed: 12/21/2022]
Abstract
Constant pH molecular dynamics offers a means to rigorously study the effects of solution pH on dynamical processes. Here, we address two critical questions arising from the most recent developments of the all-atom continuous constant pH molecular dynamics (CpHMD) method: (1) What is the effect of spatial electrostatic truncation on the sampling of protonation states? (2) Is the enforcement of electrical neutrality necessary for constant pH simulations? We first examined how the generalized reaction field and force-shifting schemes modify the electrostatic forces on the titration coordinates. Free energy simulations of model compounds were then carried out to delineate the errors in the deprotonation free energy and salt-bridge stability due to electrostatic truncation and system net charge. Finally, CpHMD titration of a mini-protein HP36 was used to understand the manifestation of the two types of errors in the calculated pK(a) values. The major finding is that enforcing charge neutrality under all pH conditions and at all time via cotitrating ions significantly improves the accuracy of protonation-state sampling. We suggest that such finding is also relevant for simulations with particle mesh Ewald, considering the known artifacts due to charge-compensating background plasma.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Jana K. Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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35
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Kim MO, Blachly PG, Kaus JW, McCammon JA. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B 2014; 119:861-72. [PMID: 25134690 PMCID: PMC4306499 DOI: 10.1021/jp505777n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
In protein–ligand binding,
the electrostatic environments
of the two binding partners may vary significantly in bound and unbound
states, which may lead to protonation changes upon binding. In cases
where ligand binding results in a net uptake or release of protons,
the free energy of binding is pH-dependent. Nevertheless, conventional
free energy calculations and molecular docking protocols typically
do not rigorously account for changes in protonation that may occur
upon ligand binding. To address these shortcomings, we present a simple
methodology based on Wyman’s binding polynomial formalism to
account for the pH dependence of binding free energies and demonstrate
its use on cucurbit[7]uril (CB[7]) host–guest systems. Using
constant pH molecular dynamics and a reference binding free energy
that is taken either from experiment or from thermodynamic integration
computations, the pH-dependent binding free energy is determined.
This computational protocol accurately captures the large pKa shifts observed experimentally upon CB[7]:guest
association and reproduces experimental binding free energies at different
levels of pH. We show that incorrect assignment of fixed protonation
states in free energy computations can give errors of >2 kcal/mol
in these host–guest systems. Use of the methods presented here
avoids such errors, thus suggesting their utility in computing proton-linked
binding free energies for protein–ligand complexes.
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Affiliation(s)
- M Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
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36
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Lee J, Miller BT, Damjanović A, Brooks BR. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. J Chem Theory Comput 2014; 10:2738-2750. [PMID: 25061443 PMCID: PMC4095908 DOI: 10.1021/ct500175m] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/21/2022]
Abstract
We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values.
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Affiliation(s)
- Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Benjamin T Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Ana Damjanović
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States ; Department of Biophysics, Johns Hopkins University , Baltimore, Maryland, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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37
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Goh G, Laricheva EN, Brooks CL. Uncovering pH-dependent transient states of proteins with buried ionizable residues. J Am Chem Soc 2014; 136:8496-9. [PMID: 24842060 PMCID: PMC4227812 DOI: 10.1021/ja5012564] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 02/04/2023]
Abstract
The role of pH in regulating biological activity is ubiquitous, and understanding pH-mediated activity has traditionally relied on analyzing static biomolecular structures of highly populated ground states solved near physiological pH. However, recent advances have shown the increasing importance of transiently populated states, the characterization of which is extremely challenging but made plausible with the development of techniques such as relaxation dispersion NMR spectroscopy. To unlock the pH dependence of these transient states with atomistic-level details, we applied the recently developed explicit solvent constant pH molecular dynamics (CPHMD(MSλD)) framework to a series of staphylococcal nuclease (SNase) mutants with buried ionizable residues and probed their dynamics in different pH environments. Among our key findings is the existence of open states in all SNase mutants containing "buried" residues with highly shifted pKa's, where local solvation around the protonation site was observed. The calculated pKa demonstrated good agreement with experimental pKa's, with a low average unsigned error of 1.3 pKa units and correlation coefficient R(2) = 0.78. Sampling both open and closed states in their respective pH range, where they are expected to be dominant, was necessary to reproduce experimental pKa's, and in the most extreme examples of pKa shifts measured, it can be interpreted that the open-state structures are transient at physiological pH, contributing a small population of 1-2%. This suggests that buried ionizable residues can trigger conformational fluctuations that may be observed as transient-state structures at physiological pH. Furthermore, the coupled relationship of both open and closed states and their role in recapitulating macroscopic experimental observables suggest that structural analysis of buried residues may benefit from looking at structural pairs, as opposed to the conventional approach of looking at a single static ground-state conformation.
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Affiliation(s)
- Garrett
B. Goh
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elena N. Laricheva
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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38
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Chen W, Morrow BH, Shi C, Shen JK. Recent development and application of constant pH molecular dynamics. MOLECULAR SIMULATION 2014; 40:830-838. [PMID: 25309035 DOI: 10.1080/08927022.2014.907492] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein-protein and protein-RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.
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Affiliation(s)
- Wei Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Brian H Morrow
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Chuanyin Shi
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jana K Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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39
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Wang B, Predeus AV, Burton ZF, Feig M. Energetic and structural details of the trigger-loop closing transition in RNA polymerase II. Biophys J 2014; 105:767-75. [PMID: 23931324 DOI: 10.1016/j.bpj.2013.05.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022] Open
Abstract
An evolutionarily conserved element in RNA polymerase II, the trigger loop (TL), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (NTP), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. In response to NTP binding, the TL undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. A computational strategy for characterizing the conformational transition pathway is presented to bridge the open and closed states of the TL. Information from a large number of independent all-atom molecular dynamics trajectories from Hamiltonian replica exchange and targeted molecular dynamics simulations is gathered together to assemble a connectivity map of the conformational transition. The results show that with a cognate NTP, TL closing should be a spontaneous process. One major intermediate state is identified along the conformational transition pathway, and the key structural features are characterized. The complete pathway from the open TL to the closed TL provides a clear picture of the TL closing.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
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40
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Abstract
RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.
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41
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Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 2014; 82:1319-31. [PMID: 24375620 DOI: 10.1002/prot.24499] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 11/13/2013] [Accepted: 12/12/2013] [Indexed: 12/14/2022]
Abstract
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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42
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Havrila M, Réblová K, Zirbel CL, Leontis NB, Šponer J. Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop. J Phys Chem B 2013; 117:14302-19. [PMID: 24144333 PMCID: PMC3946555 DOI: 10.1021/jp408530w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Nonisosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. The MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that the inability to form stable cWW geometry is an important factor in the case of the first base pair of the flexible region of the SR motif. A comparison of structural, bioinformatics, SHAPE probing, and MD simulation data reveals that explicit solvent MD simulations neatly reflect the viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Craig L. Zirbel
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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43
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Denning EJ, Thirumalai D, MacKerell AD. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure. Biophys Chem 2013; 184:8-16. [PMID: 24012912 DOI: 10.1016/j.bpc.2013.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/08/2013] [Accepted: 08/08/2013] [Indexed: 01/10/2023]
Abstract
The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.
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Affiliation(s)
- Elizabeth J Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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Garnier S, Laschewsky A, Storsberg J. Polymeric Surfactants: Novel Agents with Exceptional Properties. TENSIDE SURFACT DET 2013. [DOI: 10.3139/113.100290] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Abstract
This article presents recent progress in the field of polymeric surfactants made of permanently amphiphilic block copolymers or of stimulus-sensitive ones. We highlight key points in the design of amphiphilic macromolecules, to yield polymer surfactants with tailor-made properties, as well as recently developed and still challenging application fields for this new class of surfactants. The efficiency boosting of amphiphilic block copolymers as co-surfactants in microemulsions is discussed, as are surface modification by polymer surfactants, and stabilization of dispersions. Moreover, the use of block copolymers in nanosciences is presented, for instance as a tool for nanomaterial fabrication, or for biomedical and cosmetic applications in bio-nanotechnology. Finally, self-assembly and applications of some newly developed “exotic” amphiphilic block copolymer structures as new surface-active materials will be highlighted.
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Affiliation(s)
- S. Garnier
- Universität Potsdam, P. O. Box 6015 53, D-14415 Potsdam-Golm (Germany)
| | - A. Laschewsky
- Universität Potsdam, P. O. Box 6015 53, D-14415 Potsdam-Golm (Germany)
- Fraunhofer Institut für Angewandte Polymerforschung FhG-IAP, Geiselbergstr. 69, D-14476 Potsdam-Golm (Germany)
| | - J. Storsberg
- Fraunhofer Institut für Angewandte Polymerforschung FhG-IAP, Geiselbergstr. 69, D-14476 Potsdam-Golm (Germany)
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Nikolova EN, Goh GB, Brooks CL, Al-Hashimi HM. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. J Am Chem Soc 2013; 135:6766-9. [PMID: 23506098 DOI: 10.1021/ja400994e] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
G·C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in DNA recognition, replication, and repair. G·C Hoogsteen base pairs are thought to be stabilized by protonation of cytosine N3, which affords a second key hydrogen bond, but experimental evidence for this is sparse because the proton cannot be directly visualized by X-ray crystallography and nuclear magnetic resonance spectroscopy. Here, we combine NMR and constant pH molecular dynamics simulations to directly investigate the pKa of cytosine N3 in a chemically trapped N1-methyl-G·C Hoogsteen base pair within duplex DNA. Analysis of NMR chemical shift perturbations and NOESY data as a function of pH revealed that cytosine deprotonation is coupled to a syn-to-anti transition in N1-methyl-G, which results in a distorted Watson-Crick geometry at pH >9. A four-state analysis of the pH titration profiles yields a lower bound pKa estimate of 7.2 ± 0.1 for the G·C Hoogsteen base pair, which is in good agreement with the pKa value (7.1 ± 0.1) calculated independently using constant pH MD simulations. Based on these results and pH-dependent NMR relaxation dispersion measurements, we estimate that under physiological pH (pH 7-8), G·C Hoogsteen base pairs in naked DNA have a population of 0.02-0.002%, as compared to 0.4% for A·T Hoogsteen base pairs, and likely exist primarily as protonated species.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
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Goh GB, Knight JL, Brooks CL. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. J Phys Chem Lett 2013; 4:760-766. [PMID: 23526474 PMCID: PMC3601767 DOI: 10.1021/jz400078d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMDMSλD) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMDMSλD framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMDMSλD simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMDMSλD simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: electrostatics and solvation. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2001; Chapter 7:Unit 7.9. [PMID: 18428877 PMCID: PMC4091950 DOI: 10.1002/0471142700.nc0709s05] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics.
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