1
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Xie X, Lin S. Targeting and Manipulating Tryptophan Interactions on Proteins. ACS Chem Biol 2024; 19:1211-1213. [PMID: 38785570 DOI: 10.1021/acschembio.4c00267] [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: 05/25/2024]
Abstract
Tryptophan, commonly regarded as buried within the interior cores of proteins to maintain secondary structures, is now being recognized for its significant contributions to protein functionality. However, investigating functional tryptophan-involved interactions across the proteome and manipulating these interactions in live cells are considerable challenges. In this In Focus article, we summarize emerging advances in the field, describing innovative chemistries that leverage distinctive biochemical properties of the indole moiety for targeting and functionally manipulating tryptophan interactions.
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Affiliation(s)
- Xiao Xie
- California Institute of Quantitative Biosciences, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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2
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Li L, Han J, Lo HYG, Tam WWL, Jia H, Tse ECM, Taliaferro JM, Li Y. Symmetry-breaking malachite green as a near-infrared light-activated fluorogenic photosensitizer for RNA proximity labeling. Nucleic Acids Res 2024; 52:e36. [PMID: 38407347 DOI: 10.1093/nar/gkae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024] Open
Abstract
Cellular RNA is asymmetrically distributed in cells and the regulation of RNA localization is crucial for proper cellular functions. However, limited chemical tools are available to capture dynamic RNA localization in complex biological systems with high spatiotemporal resolution. Here, we developed a new method for RNA proximity labeling activated by near-infrared (NIR) light, which holds the potential for deep penetration. Our method, termed FAP-seq, utilizes a genetically encoded fluorogen activating protein (FAP) that selectively binds to a set of substrates known as malachite green (MG). FAP binding restricts the rotation of MG and rapidly activates its fluorescence in a wash-free manner. By introducing a monoiodo modification to MG, we created a photosensitizer (MG-HI) with the highest singlet oxygen generation ability among various MG derivatives, enabling both protein and RNA proximity labeling in live cells. New insights are provided in the transcriptome analysis with FAP-seq, while a deeper understanding of the symmetry-breaking structural arrangement of FAP-MG-HI was obtained through molecular dynamics simulations. Overall, our wash-free and NIR light-inducible RNA proximity labeling method (FAP-seq) offers a powerful and versatile approach for investigating complex mechanisms underlying RNA-related biological processes.
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Affiliation(s)
- Lan Li
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Jinghua Han
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Winnie Wai Ling Tam
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
| | - Edmund Chun Ming Tse
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
- CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong 999077, China
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Hong Kong 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories, Hong Kong 999077, China
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3
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Zhu Y, Ding W, Chen Y, Shan Y, Liu C, Fan X, Lin S, Chen PR. Genetically encoded bioorthogonal tryptophan decaging in living cells. Nat Chem 2024; 16:533-542. [PMID: 38418535 DOI: 10.1038/s41557-024-01463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Tryptophan (Trp) plays a critical role in the regulation of protein structure, interactions and functions through its π system and indole N-H group. A generalizable method for blocking and rescuing Trp interactions would enable the gain-of-function manipulation of various Trp-containing proteins in vivo, but generating such a platform remains challenging. Here we develop a genetically encoded N1-vinyl-caged Trp capable of rapid and bioorthogonal decaging through an optimized inverse electron-demand Diels-Alder reaction, allowing site-specific activation of Trp on a protein of interest in living cells. This chemical activation of a genetically encoded caged-tryptophan (Trp-CAGE) strategy enables precise activation of the Trp of interest underlying diverse important molecular interactions. We demonstrate the utility of Trp-CAGE across various protein families, such as catalase-peroxidases and kinases, as translation initiators and posttranslational modification readers, allowing the modulation of epigenetic signalling in a temporally controlled manner. Coupled with computer-aided prediction, our strategy paves the way for bioorthogonal Trp activation on more than 28,000 candidate proteins within their native cellular settings.
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Affiliation(s)
- Yuchao Zhu
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Wenlong Ding
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Ye Shan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chao Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Xinyuan Fan
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China.
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Peng R Chen
- New Cornerstone Science Laboratory, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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4
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Kletzien OA, Wuttke DS, Batey RT. The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs. Biochemistry 2024. [PMID: 38329035 DOI: 10.1021/acs.biochem.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
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5
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Schiopu I, Dragomir I, Asandei A. Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability. RSC Adv 2024; 14:5449-5460. [PMID: 38352678 PMCID: PMC10862658 DOI: 10.1039/d3ra07746b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.
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Affiliation(s)
- Irina Schiopu
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Isabela Dragomir
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Alina Asandei
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
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6
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Ali Z, Kukhta T, Trant JF, Sharma P. An Atlas of the base inter-RNA stacks involved in bacterial translation. Biophys Chem 2024; 305:107144. [PMID: 38061282 DOI: 10.1016/j.bpc.2023.107144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
Nucleobase-specific noncovalent interactions play a crucial role in translation. Herein, we provide a comprehensive analysis of the stacks between different RNA components in the crystal structures of the bacterial ribosome caught at different translation stages. Analysis of tRNA||rRNA stacks reveals distinct behaviour; both the A-and E-site tRNAs exhibit unique stacking patterns with 23S rRNA bases, while P-site tRNAs stack with 16S rRNA bases. Furthermore, E-site stacks exhibit diverse face orientations and ring topologies-rare for inter-chain RNA interactions-with higher average interaction energies than A or P-site stacks. This suggests that stacking may be essential for stabilizing tRNA progression through the E-site. Additionally, mRNA||rRNA stacks reveal other geometries, which depend on the tRNA binding site, whereas 16S rRNA||23S rRNA stacks highlight the importance of specific bases in maintaining the integrity of the translational complex by linking the two rRNAs. Furthermore, tRNA||mRNA stacks exhibit distinct geometries and energetics at the E-site, indicating their significance during tRNA translocation and elimination. Overall, both A and E-sites display a more diverse distribution of inter-RNA stacks compared to the P-site. Stacking interactions in the active ribosome are not simply accidental byproducts of biochemistry but are likely invoked to compensate and support the integrity and dynamics of translation.
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MESH Headings
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomes/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/analysis
- RNA, Messenger/metabolism
- Nucleic Acid Conformation
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; We-Spark Health Institute, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada; Binary Star Research Services, LaSalle, ON N9J 3X8, Canada.
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India; Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada.
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7
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Harini K, Sekijima M, Gromiha MM. PRA-Pred: Structure-based prediction of protein-RNA binding affinity. Int J Biol Macromol 2024; 259:129490. [PMID: 38224813 DOI: 10.1016/j.ijbiomac.2024.129490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Understanding crucial factors that affect the binding affinity of protein-RNA complexes is vital for comprehending their recognition mechanisms. This study involved compiling experimentally measured binding affinity (ΔG) values of 217 protein-RNA complexes and extracting numerous structure-based features, considering RNA, protein, and interactions between protein and RNA. Our findings indicate the significance of RNA base-step parameters, interaction energies, number of atomic contacts in the complex, hydrogen bonds, and contact potentials in understanding the binding affinity. Further, we observed that these factors are influenced by the type of RNA strand and the function of the protein in a protein-RNA complex. Multiple regression equations were developed for different classes of complexes to perform the prediction of the binding affinity between the protein and RNA. We evaluated the models using the jack-knife test and achieved an overall correlation 0.77 between the experimental and predicted binding affinities with a mean absolute error of 1.02 kcal/mol. Furthermore, we introduced a web server, PRA-Pred, intended for the prediction of protein-RNA binding affinity, and it is freely accessible through https://web.iitm.ac.in/bioinfo2/prapred/. We propose that our approach could function as a potential resource for investigating protein-RNA recognitions and developing therapeutic strategies.
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Affiliation(s)
- K Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Sekijima
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama, 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
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8
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Kumar YB, Kumar N, Vaikundamani S, Nagamani S, Mahanta HJ, Sastry GM, Sastry GN. Analyzing the aromatic-aromatic interactions in proteins: A 2ID 2.0. Int J Biol Macromol 2023; 253:127207. [PMID: 37797858 DOI: 10.1016/j.ijbiomac.2023.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/09/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - G Madhavi Sastry
- Schrödinger Inc., HITEC City, Hyderabad, Telangana 500081, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India.
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9
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Ku TH, Ram-Mohan N, Zudock EJ, Abe R, Yang S. Neutrophil Extracellular Traps have DNAzyme activity that drives bactericidal potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563618. [PMID: 37961380 PMCID: PMC10634746 DOI: 10.1101/2023.10.23.563618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The mechanisms of bacterial killing by neutrophil extracellular traps (NETs) are unclear. DNA, the largest component of NETs is believed to merely be a scaffold with minimal antimicrobial activity through the charge of the backbone. Here, we report that NETs DNA is beyond a scaffold and produces hydroxyl free radicals through the spatially concentrated G-quadruplex/hemin DNAzyme complexes, driving bactericidal effects. Immunofluorescence staining showed colocalization of G-quadruplex and hemin in extruded NETs DNA, and Amplex UltraRed assay portrayed its peroxidase activity. Proximity labeling of bacteria revealed localized concentration of radicals resulting from NETs bacterial trapping. Ex vivo bactericidal assays revealed that G-quadruplex/hemin DNAzyme is the primary driver of bactericidal activity in NETs. NETs are DNAzymes that may have important biological consequences.
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Affiliation(s)
- Ti-Hsuan Ku
- Department of Emergency Medicine, Stanford University, Stanford, CA 94305, United States
| | - Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University, Stanford, CA 94305, United States
| | - Elizabeth J Zudock
- Department of Emergency Medicine, Stanford University, Stanford, CA 94305, United States
| | - Ryuichiro Abe
- Department of Emergency Medicine, Stanford University, Stanford, CA 94305, United States
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, CA 94305, United States
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10
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Zhao L, Koseki SRT, Silverstein RA, Amrani N, Peng C, Kramme C, Savic N, Pacesa M, Rodríguez TC, Stan T, Tysinger E, Hong L, Yudistyra V, Ponnapati MR, Jacobson JM, Church GM, Jakimo N, Truant R, Jinek M, Kleinstiver BP, Sontheimer EJ, Chatterjee P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 2023; 14:6175. [PMID: 37794046 PMCID: PMC10550912 DOI: 10.1038/s41467-023-41829-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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Affiliation(s)
- Lin Zhao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Christina Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christian Kramme
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Natasha Savic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Teodora Stan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emma Tysinger
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lauren Hong
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Vivian Yudistyra
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Joseph M Jacobson
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Noah Jakimo
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Pranam Chatterjee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
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11
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Kletzien OA, Wuttke DS, Batey RT. The RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558674. [PMID: 37786719 PMCID: PMC10541603 DOI: 10.1101/2023.09.20.558674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG element within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV crosslinking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing eleven of these identified crosslink sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG element is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG element with RNA-binding properties comparable to the canonical RGG/RG element. These RGG/RG elements serve redundant functions, with neither serving as the primary RBD. While in isolation each RGG/RG element has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling binding of most of the designed RNA set with low to mid-nanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlights the perils of a reductionist approach to defining biochemical activities in this system and paves the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A. Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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12
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Foote AT, Kelm RJ. Aromatic Residues Dictate the Transcriptional Repressor and Single-Stranded DNA Binding Activities of Purine-Rich Element Binding Protein B. Biochemistry 2023; 62:2597-2610. [PMID: 37556352 DOI: 10.1021/acs.biochem.3c00204] [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: 08/11/2023]
Abstract
Purine-rich element binding protein B (Purβ) is a single-stranded DNA (ssDNA) and RNA-binding protein that functions as a transcriptional repressor of genes encoding certain muscle-restricted contractile proteins in the setting of cellular stress or tissue injury. A prior report from our laboratory implicated specific basic amino acid residues in the physical and functional interaction of Purβ with the smooth muscle-α actin gene (Acta2) promoter. Independent structural analysis of fruit fly Purα uncovered a role for several aromatic residues in the binding of this related protein to ssDNA. Herein, we examine the functional importance of a comparable set of hydrophobic residues that are positionally conserved in the repeat I (Y59), II (F155), and III (F256) domains of murine Purβ. Site-directed Y/F to alanine substitutions were engineered, and the resultant Purβ point mutants were tested in various biochemical and cell-based assays. None of the mutations affected the cellular expression, structural stability, or dimerization capacity of Purβ. However, the Y59A and F155A mutants demonstrated weaker Acta2 repressor activity in transfected fibroblasts and reduced binding affinity for the purine-rich strand of an Acta2 cis-regulatory element in vitro. Mutation of Y59 and F155 also altered the multisite binding properties of Purβ for ssDNA and diminished the interaction of Purβ with Y-box binding protein 1, a co-repressor of Acta2. Collectively, these findings suggest that some of the same aromatic residues, which govern the specific and high-affinity binding of Purβ to ssDNA, also mediate certain heterotypic protein interactions underlying the Acta2 repressor function of Purβ.
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Affiliation(s)
- Andrea T Foote
- Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
| | - Robert J Kelm
- Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
- Department of Biochemistry, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
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13
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Ali Z, Kukhta T, Jhunjhunwala A, Trant JF, Sharma P. Occurrence and classification of T-shaped interactions between nucleobases in RNA structures. RNA (NEW YORK, N.Y.) 2023; 29:1215-1229. [PMID: 37188492 PMCID: PMC10351890 DOI: 10.1261/rna.079486.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023]
Abstract
Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid-protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3261 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date data set of ≤3.5 Å resolution crystal structures deposited in the Protein Data Bank.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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14
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Ali Z, Kaur S, Kukhta T, Abu-Saleh AAAA, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA. J Phys Chem B 2023. [PMID: 37369074 DOI: 10.1021/acs.jpcb.3c02268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Sarabjeet Kaur
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Surface Chemistry and Catalysis: Characterisation and Application Team (COK-KAT), Leuven (Arenberg) Celestijnenlaan 200f─Box 2461, 3001 Leuven, Belgium
| | - Teagan Kukhta
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
| | - Abd Al-Aziz A Abu-Saleh
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
- Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
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15
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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16
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Kurup HM, Kvach MV, Harjes S, Jameson GB, Harjes E, Filichev VV. Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A. Org Biomol Chem 2023; 21:5117-5128. [PMID: 37282621 PMCID: PMC10282898 DOI: 10.1039/d3ob00392b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.
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Affiliation(s)
- Harikrishnan M Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
| | - Geoffrey B Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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17
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Harini K, Kihara D, Michael Gromiha M. PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features. Methods 2023; 213:10-17. [PMID: 36924867 PMCID: PMC10563387 DOI: 10.1016/j.ymeth.2023.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/17/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Protein-DNA interactions play an important role in various biological processes such as gene expression, replication, and transcription. Understanding the important features that dictate the binding affinity of protein-DNA complexes and predicting their affinities is important for elucidating their recognition mechanisms. In this work, we have collected the experimental binding free energy (ΔG) for a set of 391 Protein-DNA complexes and derived several structure-based features such as interaction energy, contact potentials, volume and surface area of binding site residues, base step parameters of the DNA and contacts between different types of atoms. Our analysis on relationship between binding affinity and structural features revealed that the important factors mainly depend on the number of DNA strands as well as functional and structural classes of proteins. Specifically, binding site properties such as number of atom contacts between the DNA and protein, volume of protein binding sites and interaction-based features such as interaction energies and contact potentials are important to understand the binding affinity. Further, we developed multiple regression equations for predicting the binding affinity of protein-DNA complexes belonging to different structural and functional classes. Our method showed an average correlation and mean absolute error of 0.78 and 0.98 kcal/mol, respectively, between the experimental and predicted binding affinities on a jack-knife test. We have developed a webserver, PDA-PreD (Protein-DNA Binding affinity predictor), for predicting the affinity of protein-DNA complexes and it is freely available at https://web.iitm.ac.in/bioinfo2/pdapred/.
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Affiliation(s)
- K Harini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States; Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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18
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Koseki S, Hong L, Yudistyra V, Stan T, Tysinger E, Silverstein R, Kramme C, Amrani N, Savic N, Pacesa M, Rodriguez T, Ponnapati M, Jacobson J, Church G, Truant R, Jinek M, Kleinstiver B, Sontheimer E, Chatterjee P. PAM-Flexible Genome Editing with an Engineered Chimeric Cas9. RESEARCH SQUARE 2023:rs.3.rs-2625838. [PMID: 36945419 PMCID: PMC10029082 DOI: 10.21203/rs.3.rs-2625838/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN PAM preference, with the N-terminus of Sc++, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse NNN PAMs and disease-related loci for potential therapeutic applications. In total, the unique approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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Affiliation(s)
| | | | | | | | | | | | | | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical Schoo
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19
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Ali Z, Goyal A, Jhunjhunwala A, Mitra A, Trant JF, Sharma P. Structural and Energetic Features of Base-Base Stacking Contacts in RNA. J Chem Inf Model 2023; 63:655-669. [PMID: 36635230 DOI: 10.1021/acs.jcim.2c01116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nucleobase π-π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π-π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.
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Affiliation(s)
- Zakir Ali
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ambika Goyal
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
| | - Ayush Jhunjhunwala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana500032, India
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
- Binary Star Research Services, LaSalle, OntarioN9J 3X8, Canada
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada
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20
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Wu Z, Basu S, Wu X, Kurgan L. qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids. Protein Sci 2023; 32:e4544. [PMID: 36519304 PMCID: PMC9798252 DOI: 10.1002/pro.4544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/. This new tool should be particularly useful to predict details of protein-NA interactions for large protein families and proteomes.
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Affiliation(s)
- Zhonghua Wu
- School of Mathematical Sciences and LPMCNankai UniversityTianjinChina
| | - Sushmita Basu
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Xuantai Wu
- School of Mathematical Sciences and LPMCNankai UniversityTianjinChina
| | - Lukasz Kurgan
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
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21
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Wang L, Wang Y, Wang CS, Hao Q. An Application of Dipole–Dipole Interaction Model in Stacking Dimers Including Protonated Arginine Residue. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422090205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
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Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
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23
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Urrutia KM, Xu W, Zhao L. The 5′-phosphate enhances the DNA-binding and exonuclease activities of human mitochondrial genome maintenance nuclease 1 (MGME1). J Biol Chem 2022; 298:102306. [PMID: 35934053 PMCID: PMC9460513 DOI: 10.1016/j.jbc.2022.102306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/15/2022] Open
Abstract
In higher eukaryotes, mitochondria play multiple roles in energy production, signaling, and biosynthesis. Mitochondria possess multiple copies of mitochondrial DNA (mtDNA), which encodes 37 genes that are essential for mitochondrial and cellular function. When mtDNA is challenged by endogenous and exogenous factors, mtDNA undergoes repair, degradation, and compensatory synthesis. mtDNA degradation is an emerging pathway in mtDNA damage response and maintenance. A key factor involved is the human mitochondrial genome maintenance exonuclease 1 (MGME1). Despite previous biochemical and functional studies, controversies exist regarding the polarity of MGME1-mediated DNA cleavage. Also, how DNA sequence may affect the activities of MGME1 remains elusive. Such information is not only fundamental to the understanding of MGME1 but critical for deciphering the mechanism of mtDNA degradation. Herein, we use quantitative assays to examine the effects of substrate structure and sequence on the DNA-binding and enzymatic activities of MGME1. We demonstrate that MGME1 binds to and cleaves from the 5′-end of single-stranded DNA substrates, especially in the presence of 5′-phosphate, which plays an important role in DNA binding and optimal cleavage by MGME1. In addition, MGME1 tolerates certain modifications at the terminal end, such as a 5′-deoxyribosephosphate intermediate formed in base excision repair. We show that MGME1 processes different sequences with varying efficiencies, with dT and dC sequences being the most and least efficiently digested, respectively. Our results provide insights into the enzymatic properties of MGME1 and a rationale for the coordination of MGME1 with the 3′–5′ exonuclease activity of DNA polymerase γ in mtDNA degradation.
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Affiliation(s)
- Kathleen M Urrutia
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, California, USA; Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California, USA.
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24
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Singh J, Raina R, Vinothkumar KR, Anand R. Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methyltransferases. ACS Chem Biol 2022; 17:829-839. [PMID: 35316014 DOI: 10.1021/acschembio.1c00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methylation of specific nucleotides is integral for ribosomal biogenesis and also serves as a common mechanism to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of the 30S-KsgA complex by cryo-electron microscopy, a state was captured, where KsgA juxtaposes between helices h44 and h45 of the 30S ribosome, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27, were mutated and evaluated for their methylation efficiency revealing factors that direct the enzyme to its cognate site with high fidelity. The biochemical studies show that the three-dimensional environment of the ribosome enables the interaction of select loop regions in KsgA with the ribosome helices paramount to maintain selectivity.
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Affiliation(s)
- Juhi Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Rahul Raina
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Kutti R. Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai400076, India
- DBT-Wellcome Trust India Alliance Senior Fellow, Mumbai400076, India
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25
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del Moral-Morales A, Salgado-Albarrán M, Ortiz-Gutiérrez E, Pérez-Hernández G, Soto-Reyes E. Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer. Front Genet 2022; 13:860924. [PMID: 35480330 PMCID: PMC9036480 DOI: 10.3389/fgene.2022.860924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin structure alteration and transcriptional defects that could promote malignancy. Despite that KDM4 proteins are promising drug targets in cancer therapy, only a few drugs have been described as inhibitors of these enzymes, while studies on natural compounds as possible inhibitors are still needed. Natural compounds are a major source of biologically active substances and many are known to target epigenetic processes such as DNA methylation and histone deacetylation, making them a rich source for the discovery of new histone demethylase inhibitors. Here, using transcriptomic analyses we determined that the KDM4 family is deregulated and associated with a poor prognosis in multiple neoplastic tissues. Also, by molecular docking and molecular dynamics approaches, we screened the COCONUT database to search for inhibitors of natural origin compared to FDA-approved drugs and DrugBank databases. We found that molecules from natural products presented the best scores in the FRED docking analysis. Molecules with sugars, aromatic rings, and the presence of OH or O- groups favor the interaction with the active site of KDM4 subfamily proteins. Finally, we integrated a protein-protein interaction network to correlate data from transcriptomic analysis and docking screenings to propose FDA-approved drugs that could be used as multitarget therapies or in combination with the potential natural inhibitors of KDM4 enzymes. This study highlights the relevance of the KDM4 family in cancer and proposes natural compounds that could be used as potential therapies.
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Affiliation(s)
- Aylin del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Elizabeth Ortiz-Gutiérrez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- *Correspondence: Ernesto Soto-Reyes, ; Gerardo Pérez-Hernández,
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- *Correspondence: Ernesto Soto-Reyes, ; Gerardo Pérez-Hernández,
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26
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Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J. Structural basis of R-loop recognition by the S9.6 monoclonal antibody. Nat Commun 2022; 13:1641. [PMID: 35347133 PMCID: PMC8960830 DOI: 10.1038/s41467-022-29187-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2′-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering. The S9.6 monoclonal antibody is widely used to map R-loops genome wide. Here, Bou-Nader et al., define the nucleic acid-binding specificity of S9.6 and report its crystal structures free and bound to a hybrid, which reveal the asymmetric recognition of the RNA and DNA strands and its A-form conformation.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Ankur Bothra
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA.
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27
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D'Acunto M. Quantum biology. π-π entanglement signatures in Protein-DNA interactions. Phys Biol 2022; 19. [PMID: 35263721 DOI: 10.1088/1478-3975/ac5bda] [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: 12/23/2021] [Accepted: 03/09/2022] [Indexed: 11/11/2022]
Abstract
DNA biological functions are carried out by individual proteins that interact with specific sequences along DNA to prime molecular processes required by cellular metabolism. Protein-DNA interactions include DNA replication, gene expression and its regulation, DNA repair, DNA restriction and modification by endonucleases, generally classified as enzymatic functions, or transcription factors functions. To find specific binding target sequences and finalize their activities, proteins must operate in symbiosis with cellular crowded environment identifying extremely small cognate sequences along the DNA chain, ranging from 15-20 bps for repressors to 4-6 bps for restriction enzymes in less than one second.
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Affiliation(s)
- Mario D'Acunto
- Istituto di Biofisica, Via Moruzzi 1, Pisa, 56124, ITALY
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28
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Warren GM, Meir A, Wang J, Patel DJ, Greene EC, Shuman S. Structure-activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB. Nucleic Acids Res 2021; 50:952-961. [PMID: 34967418 PMCID: PMC8789073 DOI: 10.1093/nar/gkab1270] [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: 10/27/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric helicase-nuclease that initiates homologous recombination by resecting DNA double-strand breaks. The AdnB subunit hydrolyzes ATP to drive single-nucleotide steps of 3′-to-5′ translocation of AdnAB on the tracking DNA strand via a ratchet-like mechanism. Trp325 in AdnB motif III, which intercalates into the tracking strand and makes a π stack on a nucleobase 5′ of a flipped-out nucleoside, is the putative ratchet pawl without which ATP hydrolysis is mechanically futile. Here, we report that AdnAB mutants wherein Trp325 was replaced with phenylalanine, tyrosine, histidine, leucine, or alanine retained activity in ssDNA-dependent ATP hydrolysis but displayed a gradient of effects on DSB resection. The resection velocities of Phe325 and Tyr325 mutants were 90% and 85% of the wild-type AdnAB velocity. His325 slowed resection rate to 3% of wild-type and Leu325 and Ala325 abolished DNA resection. A cryo-EM structure of the DNA-bound Ala325 mutant revealed that the AdnB motif III peptide was disordered and the erstwhile flipped out tracking strand nucleobase reverted to a continuous base-stacked arrangement with its neighbors. We conclude that π stacking of Trp325 on a DNA nucleobase triggers and stabilizes the flipped-out conformation of the neighboring nucleoside that underlies formation of a ratchet pawl.
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Affiliation(s)
- Garrett M Warren
- Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Aviv Meir
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Juncheng Wang
- Structural Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
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29
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Gigl M, Hofmann T, Frank O. NMR-Based Studies on Odorant-Melanoidin Interactions in Coffee Beverages. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15334-15344. [PMID: 34874702 DOI: 10.1021/acs.jafc.1c06163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A quantitative 1H NMR-based approach was established, which allowed the direct and noninvasive analysis of molecular interactions between key coffee odorants and high-molecular-weight (HMW) melanoidin polymers. A clear distinction between covalent and noncovalent interactions was achieved by monitoring the time dependency of odorant-polymer interactions, resulting in four scenarios: covalent, π-π, covalent and π-π-, as well as no interactions. Evaluation of temperature influence on e.g. 2-furfurylthiol (FFT), revealed an altered behavior with increased π-π stacking at lower temperatures and accelerated covalent interactions at higher temperatures. Human sensory experiments with HMW material and a coffee aroma reconstitution model showed a drastic reduction of "roasty/sulfury" aroma notes, as well as an increased "sweetish/caramel-like" flavor. The lack of interactions between the "sweetish/caramel" smelling 4-hydroxy-2,5-dimethyl-3(2H)-furanone with the HMW melanoidins in combination with the high binding affinity of coffee thiols explains the sensory evaluation and is obviously the reason for the fast disappearance of the typical "roasty/sulfury" aroma impressions of a freshly prepared coffee brew.
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Affiliation(s)
- Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Str. 34, Freising D-85354, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Str. 34, Freising D-85354, Germany
| | - Oliver Frank
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universität München, Lise-Meitner-Str. 34, Freising D-85354, Germany
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30
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Kagra D, Jangra R, Sharma P. Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA : Protein Complexes. Chemphyschem 2021; 23:e202100731. [PMID: 34747094 DOI: 10.1002/cphc.202100731] [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: 10/11/2021] [Revised: 11/02/2021] [Indexed: 11/08/2022]
Abstract
A nonredundant dataset of ∼300 high (up to 2.5 Å) resolution X-ray structures of RNA:protein complexes were analyzed for hydrogen bonds between amino-acid residues and canonical ribonucleotides (rNs). The identified 17100 contacts were classified based on the identity (rA, rC, rG or rU) and interacting fragment (base, sugar, or ribose) of the rN, the nature (polar or nonpolar) and interacting moiety (main chain or side chain) of the amino-acid residue, as well as the rN and amino-acid atoms participating in the hydrogen bonding. 80 possible hydrogen-bonding combinations (4 (rNs) X 20 (amino acids)) involve a wide variety of RNA and protein types and are present in multiple occurrences in almost all PDB files. Comparison with the analogously-selected DNA:protein complexes reveals that the absence of 2'-OH group in DNA mainly accounts for the differences in DNA:protein and RNA:protein hydrogen bonding. Search for intrinsically-stable base:amino acid pairs containing single or multiple hydrogen bonds reveals 37 unique pairs, which may act as well-defined RNA:protein interaction motifs. Overall, our work collectively analyzes the largest set of nucleic acid-protein hydrogen bonds to date, and therefore highlights several trends that may help frame structural rules governing the physiochemical characteristics of RNA:protein recognition.
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Affiliation(s)
- Deepika Kagra
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Raman Jangra
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
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31
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de Mello LR, Porosk L, Lourenço TC, Garcia BBM, Costa CAR, Han SW, de Souza JS, Langel Ü, da Silva ER. Amyloid-like Self-Assembly of a Hydrophobic Cell-Penetrating Peptide and Its Use as a Carrier for Nucleic Acids. ACS APPLIED BIO MATERIALS 2021; 4:6404-6416. [PMID: 35006917 DOI: 10.1021/acsabm.1c00601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a topical subject potentially exploitable for creating nanotherapeutics for the delivery of bioactive loads. These compounds are often classified into three major categories according to their physicochemical characteristics: cationic, amphiphilic, and hydrophobic. Among them, the group of hydrophobic CPPs has received increasing attention in recent years due to toxicity concerns posed by highly cationic CPPs. The hexapeptide PFVYLI (P, proline; F, phenylalanine; V, valine; Y, tyrosine; L, leucine; and I, isoleucine), a fragment derived from the C-terminal portion of α1-antitrypsin, is a prototypal example of hydrophobic CPP. This sequence shows reduced cytotoxicity and a capacity of nuclear localization, and its small size readily hints at its suitability as a building block to construct nanostructured materials. In this study, we examine the self-assembling properties of PFVYLI and investigate its ability to form noncovalent complexes with nucleic acids. By using a combination of biophysical tools including synchrotron small-angle X-ray scattering and atomic force microscopy-based infrared spectroscopy, we discovered that this CPP self-assembles into discrete nanofibrils with remarkable amyloidogenic features. Over the course of days, these fibrils coalesce into rodlike crystals that easily reach the micrometer range. Despite lacking cationic residues in the composition, PFVYLI forms noncovalent complexes with nucleic acids that retain β-sheet pairing found in amyloid aggregates. In vitro vectorization experiments performed with double-stranded DNA fragments indicate that complexes promote the internalization of nucleic acids, revealing that tropism toward cell membranes is preserved upon complexation. On the other hand, transfection assays with splice-correction oligonucleotides (SCOs) for luciferase expression show limited bioactivity across a narrow concentration window, suggesting that the propensity to form amyloidogenic aggregates may trigger endosomal entrapment. We anticipate that the findings presented here open perspectives for using this archetypical hydrophobic CPP in the fabrication of nanostructured scaffolds, which potentially integrate properties of amyloids and translocation capabilities of CPPs.
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Affiliation(s)
- Lucas R de Mello
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Ly Porosk
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Thiago C Lourenço
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Bianca B M Garcia
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Carlos A R Costa
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-861, Brazil
| | - Sang W Han
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Juliana S de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André 09210580, Brazil
| | - Ülo Langel
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-10691, Sweden
| | - Emerson R da Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
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32
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Wilson KA, Kung RW, D'souza S, Wetmore SD. Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA-protein complexes. Nucleic Acids Res 2021; 49:2213-2225. [PMID: 33544852 PMCID: PMC7913691 DOI: 10.1093/nar/gkab008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
A set of >300 nonredundant high-resolution RNA–protein complexes were rigorously searched for π-contacts between an amino acid side chain (W, H, F, Y, R, E and D) and an RNA nucleobase (denoted π–π interaction) or ribose moiety (denoted sugar–π). The resulting dataset of >1500 RNA–protein π-contacts were visually inspected and classified based on the interaction type, and amino acids and RNA components involved. More than 80% of structures searched contained at least one RNA–protein π-interaction, with π–π contacts making up 59% of the identified interactions. RNA–protein π–π and sugar–π contacts exhibit a range in the RNA and protein components involved, relative monomer orientations and quantum mechanically predicted binding energies. Interestingly, π–π and sugar–π interactions occur more frequently with RNA (4.8 contacts/structure) than DNA (2.6). Moreover, the maximum stability is greater for RNA–protein contacts than DNA–protein interactions. In addition to highlighting distinct differences between RNA and DNA–protein binding, this work has generated the largest dataset of RNA–protein π-interactions to date, thereby underscoring that RNA–protein π-contacts are ubiquitous in nature, and key to the stability and function of RNA–protein complexes.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ryan W Kung
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Simmone D'souza
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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33
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Lin M, Malik FK, Guo JT. A comparative study of protein-ssDNA interactions. NAR Genom Bioinform 2021; 3:lqab006. [PMID: 33655206 PMCID: PMC7902235 DOI: 10.1093/nargab/lqab006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/24/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, recombination and repair, and serve as key players in the maintenance of genomic stability. While a number of SSBs bind single-stranded DNA (ssDNA) non-specifically, the others recognize and bind specific ssDNA sequences. The mechanisms underlying this binding discrepancy, however, are largely unknown. Here, we present a comparative study of protein-ssDNA interactions by annotating specific and non-specific SSBs and comparing structural features such as DNA-binding propensities and secondary structure types of residues in SSB-ssDNA interactions, protein-ssDNA hydrogen bonding and π-π interactions between specific and non-specific SSBs. Our results suggest that protein side chain-DNA base hydrogen bonds are the major contributors to protein-ssDNA binding specificity, while π-π interactions may mainly contribute to binding affinity. We also found the enrichment of aspartate in the specific SSBs, a key feature in specific protein-double-stranded DNA (dsDNA) interactions as reported in our previous study. In addition, no significant differences between specific and non-specific groups with respect of conformational changes upon ssDNA binding were found, suggesting that the flexibility of SSBs plays a lesser role than that of dsDNA-binding proteins in conferring binding specificity.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Fareeha K Malik
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Research Center of Modeling and Simulation, National University of Science and Technology, Islamabad, 44000, Pakistan
| | - Jun-tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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34
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Tran MH, Park H, Nobles CL, Karunadharma P, Pan L, Zhong G, Wang H, He W, Ou T, Crynen G, Sheptack K, Stiskin I, Mou H, Farzan M. A more efficient CRISPR-Cas12a variant derived from Lachnospiraceae bacterium MA2020. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:40-53. [PMID: 33738137 PMCID: PMC7940699 DOI: 10.1016/j.omtn.2021.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022]
Abstract
CRISPR effector proteins introduce double-stranded breaks into the mammalian genome, facilitating gene editing by non-homologous end-joining or homology-directed repair. Unlike the more commonly studied Cas9, the CRISPR effector protein Cas12a/Cpf1 recognizes a T-rich protospacer adjacent motif (PAM) and can process its own CRISPR RNA (crRNA) array, simplifying the use of multiple guide RNAs. We observed that the Cas12a ortholog of Lachnospiraceae bacterium MA2020 (Lb2Cas12a) edited mammalian genes with efficiencies comparable to those of AsCas12a and LbCas12a. Compared to these well-characterized Cas12a orthologs, Lb2Cas12a is smaller and recognizes a narrow set of PAM TTTV. We introduced two mutations into Lb2Cas12a, Q571K and C1003Y, that increased its cleavage efficiency for a range of target sequences beyond those of the commonly used Cas12a orthologs AsCas12a and LbCas12a. In addition to the canonical TTTV PAM, this variant, Lb2-KY, also efficiently cleaved target regions with CTTN PAMs. Finally, we demonstrated that Lb2-KY ribonucleoprotein (RNP) complexes edited two hemoglobin target regions useful for correcting common forms of sickle-cell anemia more efficiently than commercial AsCas12a RNP complexes. Thus, Lb2-KY has distinctive properties useful for modifying a range of clinically relevant targets in the human genome.
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Affiliation(s)
- Mai H Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hajeung Park
- X-ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher L Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Li Pan
- Genomics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guocai Zhong
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haimin Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wenhui He
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tianling Ou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kelly Sheptack
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ian Stiskin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
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35
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Wilson KA, Wang L, Lin YC, O'Mara ML. Investigating the lipid fingerprint of SLC6 neurotransmitter transporters: a comparison of dDAT, hDAT, hSERT, and GlyT2. BBA ADVANCES 2021; 1:100010. [PMID: 37082011 PMCID: PMC10074915 DOI: 10.1016/j.bbadva.2021.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The local lipid annulus, or "fingerprint", of four SLC6 transporters (dDAT, hDAT, hSERT, and GlyT2) embedded in a complex neuronal membrane were compared and characterised using molecular dynamics. Our analysis included the development of new tools to improve membrane leaflet detection and the analysis of leaflet-dependent properties. Overall, the lipid fingerprints of the four transporters are comprised of similar lipids when grouped by headgroup or tail saturation. The enrichment and depletion of specific lipids, including sites of cholesterol contacts, varies between transporters. The subtle differences in lipid fingerprints results in varying membrane biophysical properties near the transporter. Our results highlight that the lipid-fingerprint of SLC6 transporters in complex membranes is highly dependent on membrane composition. Our results further characterize how the presence and identity of membrane proteins affects the complex interplay of lipid-protein interactions, influencing the local lipid environment and membrane biophysical properties.
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36
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D'Acunto M. Protein-DNA target search relies on quantum walk. Biosystems 2020; 201:104340. [PMID: 33387562 DOI: 10.1016/j.biosystems.2020.104340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 01/25/2023]
Abstract
Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researchers for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules have an extraordinary ability to find the target very quickly on the DNA chain, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequences on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. Focusing on the example of recognition of consensus sequences of EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during the search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) have been used for a long time to describe the Protein-DNA search strategy. QW, the quantum version of CRW, has been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to a protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by the environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) cases.
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Affiliation(s)
- Mario D'Acunto
- CNR-IBF, Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Via Moruzzi 1, 56124, Pisa, Italy.
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37
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Lacabanne D, Boudet J, Malär AA, Wu P, Cadalbert R, Salmon L, Allain FHT, Meier BH, Wiegand T. Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR. J Phys Chem B 2020; 124:11089-11097. [PMID: 33238710 PMCID: PMC7734624 DOI: 10.1021/acs.jpcb.0c08150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Protein–nucleic
acid interactions are essential in a variety
of biological events ranging from the replication of genomic DNA to
the synthesis of proteins. Noncovalent interactions guide such molecular
recognition events, and protons are often at the center of them, particularly
due to their capability of forming hydrogen bonds to the nucleic acid
phosphate groups. Fast magic-angle spinning experiments (100 kHz)
reduce the proton NMR line width in solid-state NMR of fully protonated
protein–DNA complexes to such an extent that resolved proton
signals from side-chains coordinating the DNA can be detected. We
describe a set of NMR experiments focusing on the detection of protein
side-chains from lysine, arginine, and aromatic amino acids and discuss
the conclusions that can be obtained on their role in DNA coordination.
We studied the 39 kDa enzyme of the archaeal pRN1 primase complexed
with DNA and characterize protein–DNA contacts in the presence
and absence of bound ATP molecules.
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Affiliation(s)
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Pengzhi Wu
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Loic Salmon
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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38
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Ham YH, Chan KKJ, Madej D, Lam H, Chan W. Proteomics Study of DNA–Protein Crosslinks in Methylmethanesulfonate and Fe2+-EDTA-Exposed Human Cells. Chem Res Toxicol 2020; 33:2739-2744. [DOI: 10.1021/acs.chemrestox.0c00289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yat-Hing Ham
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - K. K. Jason Chan
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Dominik Madej
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Wan Chan
- Department of Chemistry and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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39
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Hu Y, Tareen A, Sheu YJ, Ireland WT, Speck C, Li H, Joshua-Tor L, Kinney JB, Stillman B. Evolution of DNA replication origin specification and gene silencing mechanisms. Nat Commun 2020; 11:5175. [PMID: 33056978 PMCID: PMC7560902 DOI: 10.1038/s41467-020-18964-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023] Open
Abstract
DNA replication in eukaryotic cells initiates from replication origins that bind the Origin Recognition Complex (ORC). Origin establishment requires well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most eukaryotes lack sequence-specific origins. A 3.9 Å structure of S. cerevisiae ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) bound to origin DNA revealed that a loop within Orc2 inserts into a DNA minor groove and an α-helix within Orc4 inserts into a DNA major groove. Using a massively parallel origin selection assay coupled with a custom mutual-information-based modeling approach, and a separate analysis of whole-genome replication profiling, here we show that the Orc4 α-helix contributes to the DNA sequence-specificity of origins in S. cerevisiae and Orc4 α-helix mutations change genome-wide origin firing patterns. The DNA sequence specificity of replication origins, mediated by the Orc4 α-helix, has co-evolved with the gain of ORC-Sir4-mediated gene silencing and the loss of RNA interference. Contrary to most eukaryotes that lack sequence-specific origins of replication, S. cerevisiae origins are defined by specific DNA sequence motifs. Here the authors reveal that multiple subunits of ORC, including Orc2 and Orc4, contribute to the sequence-specificity of origins in S. cerevisiae.
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Affiliation(s)
- Y Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - A Tareen
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Y-J Sheu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - W T Ireland
- Department of Physics, California Institute of Technology, Pasadena, CA, 91125, USA
| | - C Speck
- DNA Replication Group, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, London, UK
| | - H Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - L Joshua-Tor
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY, 11724, USA
| | - J B Kinney
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - B Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA.
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40
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Lenz SAP, Li D, Wetmore SD. Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB. DNA Repair (Amst) 2020; 96:102944. [PMID: 33161373 DOI: 10.1016/j.dnarep.2020.102944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 01/09/2023]
Abstract
E. coli AlkB and human ALKBH2 belong to the AlkB family enzymes, which contain several α-ketoglutarate (α-KG)/Fe(II)-dependent dioxygenases that repair alkylated DNA. Specifically, the AlkB enzymes catalyze decarboxylation of α-KG to generate a high-valent Fe(IV)-oxo species that oxidizes alkyl groups on DNA adducts. AlkB and ALKBH2 have been reported to differentially repair select etheno adducts, with preferences for 1,N6-ethenoadenine (1,N6-εA) and 3,N4-ethenocytosine (3,N4-εC) over 1,N2-ethenoguanine (1,N2-εG). However, N2,3-ethenoguanine (N2,3-εG), the most common etheno adduct, is not repaired by the AlkB enzymes. Unfortunately, a structural understanding of the differential activity of E. coli AlkB and human ALKBH2 is lacking due to challenges acquiring atomistic details for a range of substrates using experiments. This study uses both molecular dynamics (MD) simulations and ONIOM(QM:MM) calculations to determine how the active site changes upon binding each etheno adduct and characterizes the corresponding catalytic impacts. Our data reveal that the preferred etheno substrates (1,N6-εA and 3,N4-εC) form favorable interactions with catalytic residues that situate the lesion near the Fe(IV)-oxo species and permit efficient oxidation. In contrast, although the damage remains correctly aligned with respect to the Fe(IV)-oxo moiety, repair of 1,N2-εG is mitigated by increased solvation of the active site and a larger distance between Fe(IV)-oxo and the aberrant carbons. Binding of non-substrate N2,3-εG in the active site disrupts key DNA-enzyme interactions, and positions the aberrant carbon atoms even further from the Fe(IV)-oxo species, leading to prohibitively high barriers for oxidative catalysis. Overall, our calculations provide the first structural insight required to rationalize the experimentally-reported substrate specificities of AlkB and ALKBH2 and thereby highlight the roles of several active site residues in the repair of etheno adducts that directly correlates with available experimental data. These proposed catalytic strategies can likely be generalized to other α-KG/Fe(II)-dependent dioxygenases that play similar critical biological roles, including epigenetic and post-translational regulation.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, 02881, USA
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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41
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Agafontsev AM, Shumilova TA, Oshchepkov AS, Hampel F, Kataev EA. Ratiometric Detection of ATP by Fluorescent Cyclophanes with Bellows-Type Sensing Mechanism. Chemistry 2020; 26:9991-9997. [PMID: 32497327 PMCID: PMC7496914 DOI: 10.1002/chem.202001523] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/01/2020] [Indexed: 12/13/2022]
Abstract
Pyrene-based cyclophanes have been synthesized with the aim to realize a bellows-type sensing mechanism for the ratiometric detection of nucleotide concentrations in a buffered aqueous solution. The sensing mechanism involves the encapsulation of a nucleobase between two pyrene rings, which affects the monomer-excimer equilibrium of the receptor in the excited state. The nature of the spacer and its connection pattern to pyrene rings have been varied to achieve high selectivity for ATP. The 1,8-substituted pyrene-based cyclophane with the 2,2'-diaminodiethylamine spacer demonstrates the best selectivity for ATP showing a 50-fold increase in the monomer-excimer emission ratio upon saturation with the nucleotide. The receptor can detect ATP within the biological concentrations range over a wide pH range. NMR and spectroscopic studies have revealed the importance of hydrogen bonding and stacking interactions for achieving a required receptor selectivity. The probe has been successfully applied for the real-time monitoring of creatine kinase activity.
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Affiliation(s)
- Aleksandr M. Agafontsev
- N. N. Vorozhtsov Institute of Organic Chemistry SB RAS9 Lavrentiev Avenue630090NovosibirskRussian Federation
- Institute of ChemistryTechnische Universität Chemnitz09107ChemnitzGermany
| | | | | | - Frank Hampel
- Department of Chemistry and PharmacyUniversity of Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
| | - Evgeny A. Kataev
- Department of Chemistry and PharmacyUniversity of Erlangen-NürnbergNikolaus-Fiebiger-Str. 1091058ErlangenGermany
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42
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Han H, Yao Y, Bhargava A, Wei Z, Tang Z, Suntivich J, Voznyy O, Robinson RD. Tertiary Hierarchical Complexity in Assemblies of Sulfur-Bridged Metal Chiral Clusters. J Am Chem Soc 2020; 142:14495-14503. [DOI: 10.1021/jacs.0c04764] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Haixiang Han
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Yuan Yao
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Anuj Bhargava
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Zheng Wei
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Zhichu Tang
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jin Suntivich
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Oleksandr Voznyy
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Richard D. Robinson
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, United States
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43
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Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC. PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Res 2020; 47:D1155-D1163. [PMID: 30395277 PMCID: PMC6323957 DOI: 10.1093/nar/gky1081] [Citation(s) in RCA: 245] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/22/2018] [Indexed: 01/01/2023] Open
Abstract
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF–targets under specific conditions.
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Affiliation(s)
- Chi-Nga Chow
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan
| | - Tzong-Yi Lee
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China
| | - Yu-Cheng Hung
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Guan-Zhen Li
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Hsin Liu
- Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Po-Li Kuo
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Han-Qin Zheng
- Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wen-Chi Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Taiwan.,Institute of Tropical Plant Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.,Department of Life Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
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44
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Lin M, Guo JT. New insights into protein-DNA binding specificity from hydrogen bond based comparative study. Nucleic Acids Res 2020; 47:11103-11113. [PMID: 31665426 PMCID: PMC6868434 DOI: 10.1093/nar/gkz963] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/25/2022] Open
Abstract
Knowledge of protein-DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein-DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein-DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-binding proteins with different degrees of binding specificity, we found that highly specific DNA-binding proteins show balanced hydrogen bonding with each of the two DNA strands while multi-specific DNA binding proteins are generally biased towards one strand. Protein-base pair hydrogen bonds, in which both bases of a base pair are involved in forming hydrogen bonds with amino acid side chains, are more prevalent in the highly specific protein-DNA complexes than those in the multi-specific group. Amino acids involved in side chain-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding proteins while multi-specific DNA-binding proteins prefer helices.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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45
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Baig KS. Interaction of enzymes with lignocellulosic materials: causes, mechanism and influencing factors. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00310-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbstractFor the production of biofuel (bioethanol), enzymatic adsorption onto a lignocellulosic biomass surface is a prior condition for the enzymatic hydrolysis process to occur. Lignocellulosic substances are mainly composed of cellulose, hemicellulose and lignin. The polysaccharide matrix (cellulose and hemicellulose) is capable of producing bioethanol. Therefore, lignin is removed or its concentration is reduced from the adsorption substrates by pretreatments. Selected enzymes are used for the production of reducing sugars from cellulosic materials, which in turn are converted to bioethanol. Adsorption of enzymes onto the substrate surface is a complicated process. A large number of research have been performed on the adsorption process, but little has been done to understand the mechanism of adsorption process. This article reviews the mechanisms of adsorption of enzymes onto the biomass surfaces. A conceptual adsorption mechanism is presented which will fill the gaps in literature and help researchers and industry to use adsorption more efficiently. The process of enzymatic adsorption starts with the reciprocal interplay of enzymes and substrates and ends with the establishment of molecular and cellular binding. The kinetics of an enzymatic reaction is almost the same as that of a characteristic chemical catalytic reaction. The influencing factors discussed in detail are: surface characteristics of the participating materials, the environmental factors, such as the associated flow conditions, temperature, concentration, etc. Pretreatment of lignocellulosic materials and optimum range of shear force and temperature for getting better results of adsorption are recommended.
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46
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Copley SD. The physical basis and practical consequences of biological promiscuity. Phys Biol 2020; 17:10.1088/1478-3975/ab8697. [PMID: 32244231 PMCID: PMC9291633 DOI: 10.1088/1478-3975/ab8697] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious "promiscuous" interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, UNITED STATES
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47
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Kagra D, Prabhakar PS, Sharma KD, Sharma P. Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations. ACS OMEGA 2020; 5:3612-3623. [PMID: 32118177 PMCID: PMC7045552 DOI: 10.1021/acsomega.9b04083] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.
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Affiliation(s)
- Deepika Kagra
- Computational
Biochemistry Laboratory, Department of Chemistry, and Centre for Advanced
Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Preethi Seelam Prabhakar
- Center
for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology
Hyderabad (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Karan Deep Sharma
- Computational
Biochemistry Laboratory, Department of Chemistry, and Centre for Advanced
Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Purshotam Sharma
- Computational
Biochemistry Laboratory, Department of Chemistry, and Centre for Advanced
Studies in Chemistry, Panjab University, Chandigarh 160014, India
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48
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Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
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Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
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Obuobi S, Tay HKL, Tram NDT, Selvarajan V, Khara JS, Wang Y, Ee PLR. Facile and efficient encapsulation of antimicrobial peptides via crosslinked DNA nanostructures and their application in wound therapy. J Control Release 2019; 313:120-130. [DOI: 10.1016/j.jconrel.2019.10.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 01/02/2023]
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Kruse H, Šponer J. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. J Phys Chem A 2019; 123:9209-9222. [PMID: 31560201 DOI: 10.1021/acs.jpca.9b05940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic.,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , 62500 Brno , Czech Republic
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