1
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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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Keith AD, Sawyer EB, Choy DCY, Xie Y, Biggs GS, Klein OJ, Brear PD, Wales DJ, Barker PD. Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins. Phys Chem Chem Phys 2024; 26:695-712. [PMID: 38053511 DOI: 10.1039/d3cp03897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
To survive, many pathogens extract heme from their host organism and break down the porphyrin scaffold to sequester the Fe2+ ion via a heme oxygenase. Recent studies have revealed that certain pathogens can anaerobically degrade heme. Our own research has shown that one such pathway proceeds via NADH-dependent heme degradation, which has been identified in a family of hemoproteins from a range of bacteria. HemS, from Yersinia enterocolitica, is the main focus of this work, along with HmuS (Yersinia pestis), ChuS (Escherichia coli) and ShuS (Shigella dysenteriae). We combine experiments, Energy Landscape Theory, and a bioinformatic investigation to place these homologues within a wider phylogenetic context. A subset of these hemoproteins are known to bind certain DNA promoter regions, suggesting not only that they can catalytically degrade heme, but that they are also involved in transcriptional modulation responding to heme flux. Many of the bacterial species responsible for these hemoproteins (including those that produce HemS, ChuS and ShuS) are known to specifically target oxygen-depleted regions of the gastrointestinal tract. A deeper understanding of anaerobic heme breakdown processes exploited by these pathogens could therefore prove useful in the development of future strategies for disease prevention.
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Affiliation(s)
- Alasdair D Keith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Elizabeth B Sawyer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Desmond C Y Choy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Yuhang Xie
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - George S Biggs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Oskar James Klein
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Brear
- Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge CB2 1GA, UK
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Barker
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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3
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Geronimo I, De Vivo M. Alchemical Free-Energy Calculations of Watson-Crick and Hoogsteen Base Pairing Interconversion in DNA. J Chem Theory Comput 2022; 18:6966-6973. [PMID: 36201305 DOI: 10.1021/acs.jctc.2c00848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hoogsteen (HG) base pairs have a transient nature and can be structurally similar to Watson-Crick (WC) base pairs, making their occurrence and thermodynamic stability difficult to determine experimentally. Herein, we employed the restrain-free-energy perturbation-release (R-FEP-R) method to calculate the relative free energy of the WC and HG base pairing modes in isolated and bound DNA systems and predict the glycosyl torsion conformational preference of purine bases. Notably, this method does not require prior knowledge of the transition pathway between the two end states. Remarkably, relatively fast convergence was reached, with results in excellent agreement with experimental data for all the examined DNA systems. The R-REP-R method successfully determined the stability of HG base pairing and more generally, the conformational preference of purine bases, in these systems. Therefore, this computational approach can help to understand the dynamic equilibrium between the WC and HG base pairing modes in DNA.
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Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, Genoa 16163, Italy
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4
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Galindo-Murillo R, Cheatham TE. Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA. J Phys Chem Lett 2022; 13:6283-6287. [PMID: 35775742 PMCID: PMC9466961 DOI: 10.1021/acs.jpclett.2c01348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Duplex DNA is modeled as canonical B-DNA displaying the characteristic Watson-Crick base pairs. A less common and short-lived pairing of the nucleobases is the Hoogsteen (HG) conformation. The low population of the HG base pairs (<1%) necessitates extended sampling times in order to analyze through unbiased molecular dynamics (MD) simulations. We have discovered that with extended sampling times using multiple independent copies of an 18-mer sequence, the MD trajectories reproduce the expected and transient HG base pairing. Consistent with experiment, the percentage of the HG events are within the range of ∼0.1-1.0% over the combined aggregate sampling time of more than 3.6 ms. We present the reliability of the current AMBER set of nucleic acid force fields and tools to accurately simulate naturally occurring base-pairing and opening events without any bias or restraints. The mechanism consists of base pair fraying, flipping of the purine, and reformation with HG base pairs.
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5
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Das S, Roy S, Bhattacharyya D. Understanding the role of non-Watson-Crick base pairs in DNA-protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation. Biopolymers 2022; 113:e23492. [PMID: 35615897 DOI: 10.1002/bip.23492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 11/06/2022]
Abstract
Specific recognition of DNA base sequences by proteins is vital for life-cycles of all organisms. In a large number of crystal structures of protein-DNA complexes, DNA conformation significantly deviates from the canonical B-DNA structure. A key question is whether such alternate conformations exist prior to protein binding and one is selected for complexation or the structure observed is induced by protein binding. Non-canonical base pairs, such as Hoogsteen base pairs, are often observed in crystal structures of protein-DNA complexes. We decided to explore whether the occurrence of such non-canonical base pairs in protein-DNA complexes is induced by the protein or is selected from pre-existing conformations. Detailed quantum chemical calculations with dispersion-corrected density functional theory (DFT-D) indicated that most of the non-canonical base pairs with DNA bases are stable even in the absence of the interacting amino acids. However, the G:G Hoogsteen base pair, which also appears in the telomere structure, appears to be unstable in the absence of other stabilizing agents, such as positively charged amino acids. Thus, the stability of many of the non-canonical base pair containing duplexes may be close to the canonical B-DNA structure and hence energetically accessible in the ground state; suggesting that the selection from pre-existing conformations may be an important mechanism for observed non-canonical base pairs in protein-DNA complexes.
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Affiliation(s)
- Soumi Das
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
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6
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Sequence dependence of transient Hoogsteen base pairing in DNA. PLoS Comput Biol 2022; 18:e1010113. [PMID: 35617357 PMCID: PMC9177043 DOI: 10.1371/journal.pcbi.1010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/08/2022] [Accepted: 04/19/2022] [Indexed: 11/19/2022] Open
Abstract
Hoogsteen (HG) base pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biological functions require HG pairs. This relevance has motivated experimental and computational investigations of the base-pairing transition. However, a systematic simulation of sequence variations has remained out of reach. Here, we employ advanced path-based methods to perform unprecedented free-energy calculations. Our methodology enables us to study the different mechanisms of purine rotation, either remaining inside or after flipping outside of the double helix. We study seven different sequences, which are neighbor variations of a well-studied A⋅T pair in A6-DNA. We observe the known effect of A⋅T steps favoring HG stability, and find evidence of triple-hydrogen-bonded neighbors hindering the inside transition. More importantly, we identify a dominant factor: the direction of the A rotation, with the 6-ring pointing either towards the longer or shorter segment of the chain, respectively relating to a lower or higher barrier. This highlights the role of DNA’s relative flexibility as a modulator of the WCF/HG dynamic equilibrium. Additionally, we provide a robust methodology for future HG proclivity studies. Recently, an alternative DNA base-pairing conformation, known as Hoogsteen (HG), has been found to coexist with the well-known Watson-Crick-Franklin (WCF) pairing. Several experimental and computational studies have focused on this heterogeneity, as it is involved in various recognition and replication processes. The WCF-to-HG transition mechanisms consist of a ±180° rotation of the purine base, occurring either inside of the double helix or while flipping temporarily outside of it. Even though molecular dynamics simulations can provide fine details about the transition pathways and their free-energy barriers, the computational cost has limited most studies to focus on only one particular chain (A6-DNA). Here, we investigate the sequence dependence of the base-pairing transition, by systematically varying the direct neighbors of a transitioning A⋅T pair; probing inside and outside pathways in seven distinct systems. We discover that triple-hydrogen-bonded neighboring base-pairs hinder the inside rotation mechanism, due to the reduced flexibility needed for internal base rotation. Across all sequences, we confirm that outside transitions have a lower free-energy barrier. Most importantly, we observe that the direction of the A rotation, with the A 6-ring pointing either towards the long or short end of the modelled DNA chain, has a determinant effect on the height of the free-energy barrier. These results point to a critical role of DNA’s small- and medium-scale flexibility in modulating the proclivity of HG base pairs; providing a handle that might be employed by several biological mechanisms.
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7
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Abstract
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We
explore the process of base-flipping for four central bases,
adenine, guanine, cytosine, and thymine, in a deoxyribonucleic acid
(DNA) duplex using the energy landscape perspective. NMR imino-proton
exchange and fluorescence correlation spectroscopy studies have been
used in previous experiments to obtain lifetimes for bases in paired
and extrahelical states. However, the difference of almost 4 orders
of magnitude in the base-flipping rates obtained by the two methods
implies that they are exploring different pathways and possibly different
open states. Our results support the previous suggestion that minor
groove opening may be favored by distortions in the DNA backbone and
reveal links between sequence effects and the direction of opening,
i.e., whether the base flips toward the major or the minor groove
side. In particular, base flipping along the minor groove pathway
was found to align toward the 5′ side of the backbone. We find
that bases align toward the 3′ side of the backbone when flipping
along the major groove pathway. However, in some cases for cytosine
and thymine, the base flipping along the major groove pathway also
aligns toward the 5′ side. The sequence effect may be caused
by the polar interactions between the flipping-base and its neighboring
bases on either of the strands. For guanine flipping toward the minor
groove side, we find that the equilibrium constant for opening is
large compared to flipping via the major groove. We find that the
estimated rates of base opening, and hence the lifetimes of the closed
state, obtained for thymine flipping through small and large angles
along the major groove differ by 6 orders of magnitude, whereas for
thymine flipping through small angles along the minor groove and large
angles along the major groove, the rates differ by 3 orders of magnitude.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - David J. Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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8
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Röder K, Wales DJ. The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules. Front Mol Biosci 2022; 9:820792. [PMID: 35155579 PMCID: PMC8829389 DOI: 10.3389/fmolb.2022.820792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
The energy landscape perspective is outlined with particular reference to biomolecules that perform multiple functions. We associate these multifunctional molecules with multifunnel energy landscapes, illustrated by some selected examples, where understanding the organisation of the landscape has provided new insight into function. Conformational selection and induced fit may provide alternative routes to realisation of multifunctionality, exploiting the possibility of environmental control and distinct binding modes.
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9
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Chakraborty D, Banerjee A, Wales DJ. Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides. J Phys Chem B 2021; 125:5809-5822. [PMID: 34037392 PMCID: PMC8279551 DOI: 10.1021/acs.jpcb.1c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
intrinsic conformational preferences of small peptides may
provide additional insight into the thermodynamics and kinetics of
protein folding. In this study, we explore the underlying energy landscapes
of two model peptides, namely, Ac-Ala-NH2 and Ac-Ser-NH2, using geometry-optimization-based tools developed within
the context of energy landscape theory. We analyze not only how side-chain
polarity influences the structural preferences of the dipeptides,
but also other emergent properties of the landscape, including heat
capacity profiles, and kinetics of conformational rearrangements.
The contrasting topographies of the free energy landscape agree with
recent results from Fourier transform microwave spectroscopy experiments,
where Ac-Ala-NH2 was found to exist as a mixture of two
conformers, while Ac-Ser-NH2 remained structurally locked,
despite exhibiting an apparently rich conformational landscape.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Atreyee Banerjee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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10
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Gillet N, Bartocci A, Dumont E. Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation. J Chem Phys 2021; 154:135103. [PMID: 33832258 DOI: 10.1063/5.0041332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.
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Affiliation(s)
- Natacha Gillet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Alessio Bartocci
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
| | - Elise Dumont
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, 46 allée d'Italie, F69364 Lyon, France
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11
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Ben Imeddourene A, Zargarian L, Buckle M, Hartmann B, Mauffret O. Slow motions in A·T rich DNA sequence. Sci Rep 2020; 10:19005. [PMID: 33149183 PMCID: PMC7642443 DOI: 10.1038/s41598-020-75645-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/12/2020] [Indexed: 01/09/2023] Open
Abstract
In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson-Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA-protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15 N labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.
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Affiliation(s)
- A Ben Imeddourene
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - L Zargarian
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - M Buckle
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - B Hartmann
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - O Mauffret
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France.
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12
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Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophys J 2020; 119:1568-1579. [PMID: 32946766 DOI: 10.1016/j.bpj.2020.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022] Open
Abstract
Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.
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Affiliation(s)
| | - Ioan Andricioaei
- Department of Chemistry; Department of Physics and Astronomy, University of California Irvine, Irvine, California.
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13
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Burke DF, Mantell RG, Pitt CE, Wales DJ. Energy Landscape for the Membrane Fusion Pathway in Influenza A Hemagglutinin From Discrete Path Sampling. Front Chem 2020; 8:575195. [PMID: 33102445 PMCID: PMC7546250 DOI: 10.3389/fchem.2020.575195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022] Open
Abstract
The conformational change associated with membrane fusion for Influenza A Hemagglutinin is investigated with a model based upon pre- and post-fusion structures of the HA2 component. We employ computational methods based on the potential energy landscape framework to obtain an initial path connecting these two end points, which provides the starting point for refinement of a kinetic transition network. Here we employ discrete path sampling, which provides access to the experimental time and length scales via geometry optimization techniques to identify local minima and the transition states that connect them. We then analyse the distinct phases of the predicted pathway in terms of structure and energetics, and compare with available experimental data and previous simulations. Our results provide the foundations for future work, which will address the effect of mutations, changes in pH, and incorporation of additional components, especially the HA1 chain and the fusion peptide.
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Affiliation(s)
- David F. Burke
- EMBL-EBI, Wellcome Genome Campus, Hinxton, United Kingdom
- David F. Burke
| | | | - Catherine E. Pitt
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: David J. Wales
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14
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Röder K, Stirnemann G, Dock-Bregeon AC, Wales DJ, Pasquali S. Structural transitions in the RNA 7SK 5' hairpin and their effect on HEXIM binding. Nucleic Acids Res 2020; 48:373-389. [PMID: 31732748 PMCID: PMC7145557 DOI: 10.1093/nar/gkz1071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 12/25/2022] Open
Abstract
7SK RNA, as part of the 7SK ribonucleoprotein complex, is crucial to the regulation of transcription by RNA-polymerase II, via its interaction with the positive transcription elongation factor P-TEFb. The interaction is induced by binding of the protein HEXIM to the 5′ hairpin (HP1) of 7SK RNA. Four distinct structural models have been obtained experimentally for HP1. Here, we employ computational methods to investigate the relative stability of these structures, transitions between them, and the effects of mutations on the observed structural ensembles. We further analyse the results with respect to mutational binding assays, and hypothesize a mechanism for HEXIM binding. Our results indicate that the dominant structure in the wild type exhibits a triplet involving the unpaired nucleotide U40 and the base pair A43-U66 in the GAUC/GAUC repeat. This conformation leads to an open major groove with enough potential binding sites for peptide recognition. Sequence mutations of the RNA change the relative stability of the different structural ensembles. Binding affinity is consequently lost if these changes alter the dominant structure.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Anne-Catherine Dock-Bregeon
- Laboratoire de Biologie Intégrative des Modèles Marins, UMR CNRS 8227, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Samuela Pasquali
- Laboratoire CiTCoM, CNRS UMR 8038, Université de Paris, 4 Avenue de l'observatoire, 75270 Paris, France
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15
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Chakraborty D, Chebaro Y, Wales DJ. A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide. Phys Chem Chem Phys 2020; 22:1359-1370. [PMID: 31854397 DOI: 10.1039/c9cp04778f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depending on the amino acid sequence, as well as the local environment, some peptides have the capability to fold into multiple secondary structures. Conformational switching between such structures is a key element of protein folding and aggregation. Specifically, understanding the molecular mechanism underlying the transition from an α-helix to a β-hairpin is critical because it is thought to be a harbinger of amyloid assembly. In this study, we explore the energy landscape for an 18-residue peptide (DP5), designed by Araki and Tamura to exhibit equal propensities for the α-helical and β-hairpin forms. We find that the degeneracy is encoded in the multifunnel nature of the underlying free energy landscape. In agreement with experiment, we also observe that mutation of tyrosine at position 12 to serine shifts the equilibrium in favor of the α-helix conformation, by altering the landscape topography. The transition from the α-helix to the β-hairpin is a complex stepwise process, and occurs via collapsed coil-like intermediates. Our findings suggest that even a single mutation can tune the emergent features of the landscape, providing an efficient route to protein design. Interestingly, the transition pathways for the conformational switch seem to be minimally perturbed upon mutation, suggesting that there could be universal microscopic features that are conserved among different switch-competent protein sequences.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - Yassmine Chebaro
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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16
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Lu W, Tang Y, Wu H, Huang H, Fu Q, Qiu J, Li H. Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter. BMC Bioinformatics 2019; 20:684. [PMID: 31874602 PMCID: PMC6929275 DOI: 10.1186/s12859-019-3258-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learning methods, Markov models, and neural networks have been employed for this problem, with encouraging results regarding their predictive accuracy; however, their performances are usually limited by the requirements of the learning model and over-fitting, which requires use of a fixed number of training features. Because most natural biological sequences have variable lengths, the sequences have to be truncated before the features are employed by the learning model, which not only leads to the loss of information but also destroys biological-sequence integrity. Results To address this problem, we propose an adaptive sequence length based on deep-learning model and integrate an energy-based filter to remove the over-fitting base pairs. Conclusions Comparative experiments conducted on an authoritative dataset RNA STRAND (RNA secondary STRucture and statistical Analysis Database) revealed a 12% higher accuracy relative to three currently used methods.
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Affiliation(s)
- Weizhong Lu
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
| | - Ye Tang
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
| | - Hongjie Wu
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China. .,Anhui Key Laboratory of Intelligent Building Energy Efficiency, Anhui Jianzhu University, Hefei, Anhui, 230601, China.
| | - Hongmei Huang
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
| | - Qiming Fu
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
| | - Jing Qiu
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
| | - Haiou Li
- School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, Jiang, 215000, China
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17
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Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, Swenson DWH. Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Res 2019; 47:11069-11076. [PMID: 31665440 PMCID: PMC6868366 DOI: 10.1093/nar/gkz837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/16/2019] [Accepted: 09/29/2019] [Indexed: 12/12/2022] Open
Abstract
DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are difficult to investigate experimentally because they occur quickly, but only rarely. To gain insight into the mechanisms for this process, we performed transition path sampling simulations on a model nucleotide sequence in which an AT pair changes from WC to HG. This transition can occur in two ways, both starting with loss of hydrogen bonds in the base pair, followed by rotation around the glycosidic bond. In one route the adenine base converts from WC to HG geometry while remaining entirely within the double helix. The other route involves the adenine leaving the confines of the double helix and interacting with water. Our results indicate that this outside route is more probable. We used transition interface sampling to compute rate constants and relative free energies for the transitions between WC and HG. Our results agree with experiments, and provide highly detailed insights into the mechanisms of this important process.
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Affiliation(s)
- Jocelyne Vreede
- Computational Chemistry, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Alberto Pérez de Alba Ortíz
- Computational Chemistry, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter G Bolhuis
- Computational Chemistry, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - David W H Swenson
- Computational Chemistry, Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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18
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Xiao S, Sharpe DJ, Chakraborty D, Wales DJ. Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes. J Phys Chem Lett 2019; 10:6771-6779. [PMID: 31609632 DOI: 10.1021/acs.jpclett.9b02356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Strand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.
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Affiliation(s)
- Shiyan Xiao
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Daniel J Sharpe
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Debayan Chakraborty
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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19
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Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophys J 2019; 117:1674-1683. [PMID: 31590890 DOI: 10.1016/j.bpj.2019.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kinetic Monte Carlo simulation, we investigate the kinetics mechanism of RNA helix-terminal basepairing. The study reveals a six-state folding scheme with three dominant folding pathways of tens, hundreds, and thousands of nanoseconds of folding timescales, respectively. The overall kinetics is rate limited by the detrapping of a misfolded state with the overall folding time of 10-5 s. Moreover, the analysis examines the different roles of the various driving forces, such as the basepairing and stacking interactions and the ion binding/dissociation effects on structural changes. The results may provide useful insights for developing a basepair opening/closing rate model and further kinetics models of large RNAs.
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20
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Chakraborty D, Wales DJ. Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling. J Chem Phys 2019; 150:125101. [DOI: 10.1063/1.5070152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Schwalb NK, Orr-Ewing AJ, Temps F. Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations. J Phys Chem B 2019; 123:2904-2914. [PMID: 30875228 DOI: 10.1021/acs.jpcb.9b02361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA structures and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. Although attempts have been made to ascribe decreased excited-state lifetimes to intrastrand charge-transfer and stacking interactions, possible influences from dynamic interstrand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP·T in Watson-Crick (WC) and Hoogsteen (HS) conformations. Although the WC conformation features slowed-down, monomer-like electronic relaxation in τ ∼ 1.6 ns toward ground-state recovery and triplet formation, the dynamics associated with 2AP·T in the HS motif exhibit faster deactivation in τ ∼ 70 ps. As recent research has revealed abundant transient interstrand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramolecular photophysical mechanisms are discussed in terms of a proposed excited-state double-proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Katharina Röttger
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany.,School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Rebecca A Ingle
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Hugo J B Marroux
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Mats Bohnsack
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Nina K Schwalb
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
| | - Andrew J Orr-Ewing
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
| | - Friedrich Temps
- Institute of Physical Chemistry , Christian-Albrechts-University Kiel , Olshausenstr. 40 , 24098 Kiel , Germany
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22
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The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. Methods Mol Biol 2019; 2022:255-290. [PMID: 31396907 DOI: 10.1007/978-1-4939-9608-7_11] [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] [Indexed: 12/20/2022]
Abstract
In the past decade, great progress has been made in the development of enhanced sampling methods, aimed at overcoming the time-scale limitations of molecular dynamics (MD) simulations. Many sampling schemes rely on adding an external bias to favor the sampling of transitions and to estimate the underlying free energy landscape. Nevertheless, sampling molecular processes described by many order parameters, or collective variables (CVs), such as complex biomolecular transitions, remains often very challenging. The computational cost has a prohibitive scaling with the dimensionality of the CV-space. Inspiration can be taken from methods that focus on localizing transition pathways: the CV-space can be projected onto a path-CV that connects two stable states, and a bias can be exerted onto a one-dimensional parameter that captures the progress of the transition along the path-CV. In principle, such a sampling scheme can handle an arbitrarily large number of CVs. A standard enhanced sampling technique combined with an adaptive path-CV can then locate the mean transition pathway and obtain the free energy profile along the path. In this chapter, we discuss the adaptive path-CV formalism and its numerical implementation. We apply the path-CV with several enhanced sampling methods-steered MD, metadynamics, and umbrella sampling-to a biologically relevant process: the Watson-Crick to Hoogsteen base-pairing transition in double-stranded DNA. A practical guide is provided on how to recognize and circumvent possible pitfalls during the calculation of a free energy landscape that contains multiple pathways. Examples are presented on how to perform enhanced sampling simulations using PLUMED, a versatile plugin that can work with many popular MD engines.
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23
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Yang C, Kim E, Lim M, Pak Y. Computational Probing of Watson-Crick/Hoogsteen Breathing in a DNA Duplex Containing N1-Methylated Adenine. J Chem Theory Comput 2018; 15:751-761. [PMID: 30501194 DOI: 10.1021/acs.jctc.8b00936] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e., Watson-Crick (WC)-like and Hoogsteen (HG)-like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A). For the current free energy computation, a variant of well-tempered metadynamics simulation was extensively performed for a total of 40 μs to produce free energy surfaces. The free energy profile indicated that, upon the chemical modification of adenine, the HG bp (m1A·T) was located in the most favorable conformation (96.7%); however, the canonical WC bp (m1A·T) was distorted into two WC-like bps of WC* (2.8%) and WC** (0.5%). The conformational exchange between these two minor WC-like bps occurs with the first hundred nanoseconds. The transition between WC-like and HG bp features multiple transition pathways displaying various extents of base flipping in combination with glycosidic rotation. Analysis of the simulated ensemble showed that the m1A-induced changes of the backbone and sugar pucker were in a reasonable agreement with previous results inferred from NMR experiments. Also, this study revealed that the formation of the stable HG bp upon the mutation alters the characteristics of dynamic fluctuations of the neighboring WC residues of m1A. We expect this simulation approach to be a robust computational scheme to complement and guide future high-resolution experiments on many outstanding issues of duplex DNA breathing.
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Affiliation(s)
- Changwon Yang
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Eunae Kim
- College of Pharmacy , Chosun University , Gwangju 61452 , South Korea
| | - Manho Lim
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials , Pusan National University , Busan 46241 , South Korea
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24
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Kingsland A, Maibaum L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J Phys Chem B 2018; 122:12251-12259. [DOI: 10.1021/acs.jpcb.8b06007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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25
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Neelamraju S, Gosavi S, Wales DJ. Energy Landscape of the Designed Protein Top7. J Phys Chem B 2018; 122:12282-12291. [DOI: 10.1021/acs.jpcb.8b08499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sridhar Neelamraju
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka 560065, India
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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26
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Cai Y, Cheng L. Single-root networks for describing the potential energy surface of Lennard-Jones clusters. J Chem Phys 2018; 149:084102. [PMID: 30193512 DOI: 10.1063/1.5043330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Potential energy surface (PES) holds the key in understanding a number of atomic clusters or molecular phenomena. However, due to the high dimension and incredible complexity of PES, only indirect methods can be used to characterize a PES of a given system in general. In this paper, a branched dynamic lattice searching method was developed to travel the PES, which was described in detail by a single-root network (SRN). The advantage of SRN is that it reflects the topological relation between different conformations and highlights the size of each structure energy trap. On the basis of SRN, to demonstrate how to transform one conformation to another, the transition path that connects two local minima in the PES was constructed. Herein, we take Lennard-Jones (LJ) clusters at the sizes of 38, 55, and 75 as examples. It is found that the PES of these three clusters have many local funnels and each local funnel represents one morphology. If a morphology is located more frequently, it will lie in a larger local funnel. Besides, certain steps of the transition path were generated successfully, such as changing from icosahedral to truncated octahedral of the LJ38-cluster. Though we do not exhibit all the parts of the PES or all transition paths, this method indeed works well in the local area and can be used more widely.
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Affiliation(s)
- Yinjiang Cai
- School of Chemistry and Chemical Engineering, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Longjiu Cheng
- School of Chemistry and Chemical Engineering, Anhui University, Hefei, Anhui 230601, People's Republic of China
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27
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Elenewski JE, Velizhanin KA, Zwolak M. A spin-1 representation for dual-funnel energy landscapes. J Chem Phys 2018; 149:035101. [PMID: 30037251 PMCID: PMC7723752 DOI: 10.1063/1.5036677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model-left, right, and unstructured-can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 kBT to 0.3 kBT along the left-to-right interconversion pathway.
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Affiliation(s)
- Justin E. Elenewski
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
- Maryland Nanocenter, University of Maryland, College Park, MD 20742, USA
| | | | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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28
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Klimavicz JS, Röder K, Wales DJ. Energy Landscapes of Mini-Dumbbell DNA Octanucleotides. J Chem Theory Comput 2018; 14:3870-3876. [PMID: 29792700 DOI: 10.1021/acs.jctc.8b00262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-stranded DNA structures play a significant role in biological systems, in particular during replication, translation, and DNA repair. Tracts of simple repetitive DNA are associated with slipped-strand mispairing, which can lead to genetic diseases. Recent NMR studies of TTTA and CCTG repeats have shown that these sequences form mini-dumbbells (MDBs), leading to frameshift mutations. Here we explore the energy landscapes of (CCTG)2 and (TTTA)2, which are currently the smallest known molecules to form MDBs. While (CCTG)2 MDBs are stable, (TTTA)2 exhibits numerous other structures with lower energies. A key factor identified in the stabilization of MDB structures is the bonding strength between residues 1 and 4, and 5 and 8.
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Affiliation(s)
- James S Klimavicz
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.,Department of Entomology , Iowa State University , Ames , Iowa 50011 , United States
| | - Konstantin Röder
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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29
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Modulation of Hoogsteen dynamics on DNA recognition. Nat Commun 2018; 9:1473. [PMID: 29662229 PMCID: PMC5902632 DOI: 10.1038/s41467-018-03516-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
In naked duplex DNA, G–C and A–T Watson-Crick base pairs exist in dynamic equilibrium with their Hoogsteen counterparts. Here, we used nuclear magnetic resonance (NMR) relaxation dispersion and molecular dynamics (MD) simulations to examine how Watson-Crick/Hoogsteen dynamics are modulated upon recognition of duplex DNA by the bisintercalator echinomycin and monointercalator actinomycin D. In both cases, DNA recognition results in the quenching of Hoogsteen dynamics at base pairs involved in intermolecular base-specific hydrogen bonds. In the case of echinomycin, the Hoogsteen population increased 10-fold for base pairs flanking the chromophore most likely due to intermolecular stacking interactions, whereas actinomycin D minimally affected Hoogsteen dynamics at other sites. Modulation of Hoogsteen dynamics at binding interfaces may be a general phenomenon with important implications for DNA–ligand and DNA–protein recognition. DNA is found in a dynamic equilibrium between standard Watson-Crick (WC) base pairs and non-standard Hoogsteen (HG) base pairs. Here the authors describe the influence of echinomycin and actinomycin D ligands binding on the HG-WC base pair dynamics in DNA.
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30
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Abstract
The aggregation of the Aβ peptide (Aβ1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves the consecutive addition of monomers to one end of the growing fibril. The aggregation process proceeds in a stop-and-go fashion and may involve off-pathway aggregates, complicating experimental and computational studies. Here we present exploration of a well-defined region in the free and potential energy landscapes for the Aβ17-42 pentamer. We find that the ideal aggregation process agrees with the previously reported dock-lock mechanism. We also analyze a large number of additional stable structures located on the multifunnel energy landscape, which constitute kinetic traps. The key contributors to the formation of such traps are misaligned strong interactions, for example the stacking of F19 and F20, as well as entropic contributions. Our results suggest that folding templates for aggregation are a necessity and that aggregation studies could employ such species to obtain a more detailed description of the process.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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