1
|
Sha W, Gong C, Xiao G, Hou C, Ren J. Interaction-based screening, Monte Carlo Bayesian inference-based de novo design and in vitro verification of adenine-binding peptide. Food Chem 2024; 448:139076. [PMID: 38537545 DOI: 10.1016/j.foodchem.2024.139076] [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: 12/09/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/24/2024]
Abstract
One of the main reasons for hyperuricemia is high purine intake. The primary strategy for treating hyperuricemia is blocking the purine metabolism enzyme. However, by binding the purine bases directly, we suggested a unique therapeutic strategy that might interfere with purine metabolism. There have been numerous reports of extensive interactions between proteins and purine bases. Adenine, constituting numerous protein co-factors, can interact with the adenine-binding motif. Using Bayesian Inference and Markov chain Monte Carlo sampling, we created a novel adenine-binding peptide Ile-Tyr-Val-Thr based on the structure of the adenine-binding motifs. Ile-Tyr-Val-Thr generates a semi-pocket that can clip the adenine within, as demonstrated by docking. Then, using thermodynamic techniques, the interaction between Ile-Tyr-Val-Thr and adenine was confirmed. The KD value is 1.50e-5 (ΔH = -20.2 kJ/mol and ΔG = -27.6 kJ/mol), indicating the high affinity. In brief, the adenine-binding peptide Ile-Tyr-Val-Thr may help lower uric acid level by blocking the absorption of food-derived adenine.
Collapse
Affiliation(s)
- Wanqian Sha
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Congcong Gong
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ganhong Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chuanli Hou
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
| |
Collapse
|
2
|
Zheng Z, Goncearenco A, Berezovsky IN. Back in time to the Gly-rich prototype of the phosphate binding elementary function. Curr Res Struct Biol 2024; 7:100142. [PMID: 38655428 PMCID: PMC11035071 DOI: 10.1016/j.crstbi.2024.100142] [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: 12/30/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
Binding of nucleotides and their derivatives is one of the most ancient elementary functions dating back to the Origin of Life. We review here the works considering one of the key elements in binding of (di)nucleotide-containing ligands - phosphate binding. We start from a brief discussion of major participants, conditions, and events in prebiotic evolution that resulted in the Origin of Life. Tracing back to the basic functions, including metal and phosphate binding, and, potentially, formation of primitive protein-protein interactions, we focus here on the phosphate binding. Critically assessing works on the structural, functional, and evolutionary aspects of phosphate binding, we perform a simple computational experiment reconstructing its most ancient and generic sequence prototype. The profiles of the phosphate binding signatures have been derived in form of position-specific scoring matrices (PSSMs), their peculiarities depending on the type of the ligands have been analyzed, and evolutionary connections between them have been delineated. Then, the apparent prototype that gave rise to all relevant phosphate-binding signatures had also been reconstructed. We show that two major signatures of the phosphate binding that discriminate between the binding of dinucleotide- and nucleotide-containing ligands are GxGxxG and GxxGxG, respectively. It appears that the signature archetypal for dinucleotide-containing ligands is more generic, and it can frequently bind phosphate groups in nucleotide-containing ligands as well. The reconstructed prototype's key signature GxGGxG underlies the role of glycine residues in providing flexibility and interactions necessary for binding the phosphate groups. The prototype also contains other ancient amino acids, valine, and alanine, showing versatility towards evolutionary design and functional diversification.
Collapse
Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N. Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
| |
Collapse
|
3
|
Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J Chem Inf Model 2024; 64:2084-2100. [PMID: 38456842 DOI: 10.1021/acs.jcim.3c01969] [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] [Indexed: 03/09/2024]
Abstract
The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment-lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein-ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.
Collapse
Affiliation(s)
- Omeir Khan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria Lazou
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Diane Joseph-McCarthy
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Sandor Vajda
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| |
Collapse
|
4
|
Kramer DJ, Johnson AA. Apigenin: a natural molecule at the intersection of sleep and aging. Front Nutr 2024; 11:1359176. [PMID: 38476603 PMCID: PMC10929570 DOI: 10.3389/fnut.2024.1359176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024] Open
Abstract
NAD+, a pivotal coenzyme central to metabolism, exhibits a characteristic decline with age. In mice, NAD+ levels can be elevated via treatment with apigenin, a natural flavonoid that inhibits the NAD+-consuming glycoprotein CD38. In animal models, apigenin positively impacts both sleep and longevity. For example, apigenin improves learning and memory in older mice, reduces tumor proliferation in a mouse xenograft model of triple-negative breast cancer, and induces sedative effects in mice and rats. Moreover, apigenin elongates survival in fly models of neurodegenerative disease and apigenin glycosides increase lifespan in worms. Apigenin's therapeutic potential is underscored by human clinical studies using chamomile extract, which contains apigenin as an active ingredient. Collectively, chamomile extract has been reported to alleviate anxiety, improve mood, and relieve pain. Furthermore, dietary apigenin intake positively correlates with sleep quality in a large cohort of adults. Apigenin's electron-rich flavonoid structure gives it strong bonding capacity to diverse molecular structures across receptors and enzymes. The effects of apigenin extend beyond CD38 inhibition, encompassing agonistic and antagonistic modulation of various targets, including GABA and inflammatory pathways. Cumulatively, a large body of evidence positions apigenin as a unique molecule capable of influencing both aging and sleep. Further studies are warranted to better understand apigenin's nuanced mechanisms and clinical potential.
Collapse
|
5
|
Maity D, Singh D, Bandhu A. Mce1R of Mycobacterium tuberculosis prefers long-chain fatty acids as specific ligands: a computational study. Mol Divers 2023; 27:2523-2543. [PMID: 36385433 DOI: 10.1007/s11030-022-10566-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
The mce1 operon of Mycobacterium tuberculosis, which codes the Mce1 transporter, facilitates the transport of fatty acids. Fatty acids are one of the major sources for carbon and energy for the pathogen during its intracellular survival and pathogenicity. The mce1 operon is transcriptionally regulated by Mce1R, a VanR-type regulator, which could bind specific ligands and control the expression of the mce1 operon accordingly. This work reports computational identification of Mce1R-specific ligands. Initially by employing cavity similarity search algorithm by the ProBis server, the cavities of the proteins similar to that of Mce1R and the bound ligands were identified from which fatty acids were selected as the potential ligands. From the earlier-generated monomeric structure, the dimeric structure of Mce1R was then modeled by the GalaxyHomomer server and validated computationally to use in molecular docking and molecular dynamics simulation analysis. The fatty acid ligands were found to dock within the cavity of Mce1R and the docked complexes were subjected to molecular dynamics simulation to explore their stabilities and other dynamic properties. The data suggest that Mce1R preferably binds to long-chain fatty acids and undergoes distinct structural changes upon binding.
Collapse
Affiliation(s)
- Dipanwita Maity
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Dheeraj Singh
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India
| | - Amitava Bandhu
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, Telangana, 506004, India.
| |
Collapse
|
6
|
Gade M, Gardner JM, Jain P, Laurino P. Nucleoside-Driven Specificity of DNA Methyltransferase. Chembiochem 2023; 24:e202300094. [PMID: 37548117 DOI: 10.1002/cbic.202300094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
We have studied the adenosine binding specificities of two bacterial DNA methyltransferases, Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While they have similar cofactor binding pocket interactions, experimental data showed different specificity for novel S-nucleobase-l-methionine cofactors (SNMs; N=guanosyl, cytidyl, uridyl). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-l-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data prove catalytically productive methylation by the M.HhaI binding pocket for all the SNMs. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.
Collapse
Affiliation(s)
- Madhuri Gade
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Jasmine M Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Prashant Jain
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| |
Collapse
|
7
|
Zhao Z, Bourne PE. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett 2023; 14:1503-1508. [PMID: 37974950 PMCID: PMC10641887 DOI: 10.1021/acsmedchemlett.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first created a kinase structure-assay database (KSAD) containing 2705 nM ligand-bound kinase complexes. Then, using KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs.
Collapse
Affiliation(s)
- Zheng Zhao
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| | - Philip E. Bourne
- School of Data Science and Department
of Biomedical Engineering, University of
Virginia, Charlottesville, Virginia 22904, United States
| |
Collapse
|
8
|
Iyyappan Y, Dhayabaran V, Elayappan M, Chaudhary SK, Palaniappan C, Kanagaraj S. Functional characterization of a hypothetical protein (TTHA1873) from Thermus thermophilus. Proteins 2023; 91:1427-1436. [PMID: 37254593 DOI: 10.1002/prot.26530] [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: 02/13/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023]
Abstract
Thermus thermophilus is an extremely thermophilic organism that thrives at a temperature of 65°C. T. thermophilus genome has ~2218 genes, out of which 66% (1482 genes) have been annotated, and the remaining 34% (736 genes) are assigned as hypothetical proteins. In this work, biochemical and biophysical experiments were performed to characterize the hypothetical protein TTHA1873 from T. thermophilus. The hypothetical protein TTHA1873 acts as a nuclease, which indiscreetly cuts methylated and non-methylated DNA in divalent metal ions and relaxes the plasmid DNA in the presence of ATP. The chelation of metal ions with EDTA inhibits its activity. These results suggest that the hypothetical protein TTHA1873 would be a CRISPR-associated protein with non-specific DNase activity and ATP-dependent DNA-relaxing activity.
Collapse
Affiliation(s)
- Yuvaraj Iyyappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- National Institute for Plant Biotechnology, New Delhi, India
| | - Vaigundan Dhayabaran
- Genomics and Central Research Laboratory, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, India
| | - Mohanapriya Elayappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| | - Santosh Kumar Chaudhary
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Chemical Biology and Therapeutics Sciences, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chandrasekaran Palaniappan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sekar Kanagaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
| |
Collapse
|
9
|
Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
Collapse
|
10
|
The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus. Proc Natl Acad Sci U S A 2022; 119:e2207505119. [PMID: 36161908 DOI: 10.1073/pnas.2207505119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus, an opportunistic pathogen responsible for pulmonary infections, contains genes predicted to encode two steroid catabolic pathways: a cholesterol catabolic pathway similar to that of Mycobacterium tuberculosis and a 4-androstenedione (4-AD) catabolic pathway. Consistent with this prediction, M. abscessus grew on both steroids. In contrast to M. tuberculosis, Rhodococcus jostii RHA1, and other Actinobacteria, the cholesterol and 4-AD catabolic gene clusters of the M. abscessus complex lack genes encoding HsaD, the meta-cleavage product (MCP) hydrolase. However, M. abscessus ATCC 19977 harbors two hsaD homologs elsewhere in its genome. Only one of the encoded enzymes detectably transformed steroid metabolites. Among tested substrates, HsaDMab and HsaDMtb of M. tuberculosis had highest substrate specificities for MCPs with partially degraded side chains thioesterified with coenzyme A (kcat/KM = 1.9 × 104 and 5.7 × 103 mM-1s-1, respectively). Consistent with a dual role in cholesterol and 4-AD catabolism, HsaDMab also transformed nonthioesterified substrates efficiently, and a ΔhsaD mutant of M. abscessus grew on neither steroid. Interestingly, both steroids prevented growth of the mutant on acetate. The ΔhsaD mutant of M. abscessus excreted cholesterol metabolites with a fully degraded side chain, while the corresponding RHA1 mutant excreted metabolites with partially degraded side chains. Finally, the ΔhsaD mutant was not viable in macrophages. Overall, our data establish that the cholesterol and 4-AD catabolic pathways of M. abscessus are unique in that they converge upstream of where this occurs in characterized steroid-catabolizing bacteria. The data further indicate that cholesterol is a substrate for intracellular bacteria and that cholesterol-dependent toxicity is not strictly dependent on coenzyme A sequestration.
Collapse
|
11
|
Yang L, He W, Yun Y, Gao Y, Zhu Z, Teng M, Liang Z, Niu L. Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:765-779. [PMID: 35288344 PMCID: PMC9881048 DOI: 10.1016/j.gpb.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/30/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023]
Abstract
Uncovering conserved 3D protein-ligand binding patterns on the basis of functional groups (FGs) shared by a variety of small molecules can greatly expand our knowledge of protein-ligand interactions. Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature, large-scale identification and evaluation of FG-based 3D binding motifs are still lacking. Here, we propose a computational method, Automatic FG-based Three-dimensional Motif Extractor (AFTME), for automatic mapping of 3D motifs to different FGs of a specific ligand. Applying our method to 233 naturally-occurring ligands, we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets. Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs. Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities. Finally, we show that our FG-motif map can be used to nominate FGs that potentially bind to specific drug targets, thus providing useful insights and guidance for rational design of small-molecule drugs.
Collapse
Affiliation(s)
- Liu Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Wei He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Yuehui Yun
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Yongxiang Gao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhongliang Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Maikun Teng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China
| | - Zhi Liang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| | - Liwen Niu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei 230026, China.
| |
Collapse
|
12
|
Scott JA, Soto-Velasquez M, Hayes MP, LaVigne JE, Miller HR, Kaur J, Ejendal KFK, Watts VJ, Flaherty DP. Optimization of a Pyrimidinone Series for Selective Inhibition of Ca 2+/Calmodulin-Stimulated Adenylyl Cyclase 1 Activity for the Treatment of Chronic Pain. J Med Chem 2022; 65:4667-4686. [PMID: 35271288 PMCID: PMC9390083 DOI: 10.1021/acs.jmedchem.1c01759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Adenylyl cyclase type 1 (AC1) is involved in signaling for chronic pain sensitization in the central nervous system and is an emerging target for the treatment of chronic pain. AC1 and a closely related isoform AC8 are also implicated to have roles in learning and memory signaling processes. Our team has carried out cellular screening for inhibitors of AC1 yielding a pyrazolyl-pyrimidinone scaffold with low micromolar potency against AC1 and selectivity versus AC8. Structure-activity relationship (SAR) studies led to analogues with cellular IC50 values as low as 0.25 μM, selectivity versus AC8 and other AC isoforms as well as other common neurological targets. A representative analogue displayed modest antiallodynic effects in a mouse model of inflammatory pain. This series represents the most potent and selective inhibitors of Ca2+/calmodulin-stimulated AC1 activity to date with improved drug-like physicochemical properties making them potential lead compounds for the treatment of inflammatory pain.
Collapse
Affiliation(s)
- Jason A Scott
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Monica Soto-Velasquez
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael P Hayes
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Justin E LaVigne
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Heath R Miller
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jatinder Kaur
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karin F K Ejendal
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Drug Discovery, West Lafayette, Indiana 47907, United States
- Purdue Institute for Integrative Neuroscience, 207 South Martin Jischke Dr. West Lafayette, Indiana 47907, United States
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Drug Discovery, West Lafayette, Indiana 47907, United States
- Purdue Institute for Integrative Neuroscience, 207 South Martin Jischke Dr. West Lafayette, Indiana 47907, United States
| |
Collapse
|
13
|
Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
Collapse
Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
| |
Collapse
|
14
|
Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A. Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res 2021; 49:7139-7153. [PMID: 34125892 PMCID: PMC8266621 DOI: 10.1093/nar/gkab486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson–Crick base pair to junction J2. Xanthine inserts between a G–U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
Collapse
Affiliation(s)
- Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
15
|
Rachadech W, Kato Y, Abou El-Magd RM, Shishido Y, Kim SH, Sogabe H, Maita N, Yorita K, Fukui K. P219L substitution in human D-amino acid oxidase impacts the ligand binding and catalytic efficiency. J Biochem 2021; 168:557-567. [PMID: 32730563 DOI: 10.1093/jb/mvaa083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Human D-amino acid oxidase (DAO) is a flavoenzyme that is implicated in neurodegenerative diseases. We investigated the impact of replacement of proline with leucine at Position 219 (P219L) in the active site lid of human DAO on the structural and enzymatic properties, because porcine DAO contains leucine at the corresponding position. The turnover numbers (kcat) of P219L were unchanged, but its Km values decreased compared with wild-type, leading to an increase in the catalytic efficiency (kcat/Km). Moreover, benzoate inhibits P219L with lower Ki value (0.7-0.9 µM) compared with wild-type (1.2-2.0 µM). Crystal structure of P219L in complex with flavin adenine dinucleotide (FAD) and benzoate at 2.25 Å resolution displayed conformational changes of the active site and lid. The distances between the H-bond-forming atoms of arginine 283 and benzoate and the relative position between the aromatic rings of tyrosine 224 and benzoate were changed in the P219L complex. Taken together, the P219L substitution leads to an increase in the catalytic efficiency and binding affinity for substrates/inhibitors due to these structural changes. Furthermore, an acetic acid was located near the adenine ring of FAD in the P219L complex. This study provides new insights into the structure-function relationship of human DAO.
Collapse
Affiliation(s)
- Wanitcha Rachadech
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan.,Division of Chemistry, Faculty of Science, Udon Thani Rajabhat University, 64 Thahan Road, Muang, Udon Thani 41000, Thailand
| | - Yusuke Kato
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Rabab M Abou El-Magd
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Yuji Shishido
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Soo Hyeon Kim
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Hirofumi Sogabe
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Nobuo Maita
- Division of Disease Proteomics, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kazuko Yorita
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Kiyoshi Fukui
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| |
Collapse
|
16
|
Francis S, Rajith L. Selective Fluorescent Sensing of Adenine Via the Emissive Enhancement of a Simple Cobalt Porphyrin. J Fluoresc 2021; 31:577-586. [PMID: 33481138 DOI: 10.1007/s10895-021-02685-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/11/2021] [Indexed: 11/24/2022]
Abstract
Porphyrins absorb strongly in the visible region and are also excellent fluorophores that emit in the visible region that make them excellent candidates for fluorescence sensing and in vivo imaging. This work describes the fluorescence determination of adenine using cobalt complex of a simple porphyrin. Tetraphenylporphyrin (TPP) and tetraphenylpophyrinatocobalt(II) (CoTPP) were synthesized and characterised. TPP on metallation with cobalt resulted in the red shift of fluorescence emission in the region 652 nm and 716 nm and showed an enhancement in the emission peaks with the addition of the nucleobase, adenine. CoTPP is found to be an efficient fluorescent sensor for adenine in DMF solvent. The fluorescence enhancement is due to the formation of the ground state complex formation between adenine and CoTPP, which is supported by experimental evidences from UV- visible spectra, time resolved fluorescence life time measurements etc. The detection limit of adenine was found to be 4.2 μM using the CoTPP fluorescent probe. The proposed sensor is found to be highly selective for adenine in presence of other nitrogen bases like guanine, cytosine, uracil, thymine, alanine, histidine etc. in 1:1 concentration.
Collapse
Affiliation(s)
- Shijo Francis
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala, 682022, India
| | - Leena Rajith
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
| |
Collapse
|
17
|
Brzezinski K. S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains. Biomolecules 2020; 10:biom10121682. [PMID: 33339190 PMCID: PMC7765604 DOI: 10.3390/biom10121682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022] Open
Abstract
S-adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S-adenosyl-l-homocysteine or adenosine and the second domain binds the NAD+ cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N-glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.
Collapse
Affiliation(s)
- Krzysztof Brzezinski
- Laboratory of Structural Microbiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
18
|
Sheet T, Banerjee R. Design of a Peptide-Based Model Leads for Scavenging Anions. ACS OMEGA 2020; 5:9759-9767. [PMID: 32391463 PMCID: PMC7203709 DOI: 10.1021/acsomega.9b04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Among several peptide-based anion recognition motifs, the "CαNN" motif containing C-1 α, N0, and N+1 of three consecutive residues is unique in its mode of interaction. Having a spatial geometry of βαα or βαβ, this motif occurs in the N terminus of a helix and often found at the functional interface of a protein, mediating crucial biological significance upon interaction with anion(s). The interaction of anion(s) with chimeric peptide sequences containing the naturally occurring "CαNN" motif (CPS224Ac, CPS226, and CPS228) reported in our previous attempts strongly confirms that the information regarding the interaction is embedded within the local sequences of the motif segment. At these prevailing circumstances, an effort has been pursued to design novel scaffolds based on the "CαNN" motif for achieving better recognition of anion(s). Exploring the existing data set of the "CαNN" motif available in the FSSP database, four novel peptide-based scaffolds have been designed (DS1, DS2, DS3, and DS4), and preliminary screenings have been performed using computational approaches. Our initial work suggests that two (DS1 and DS3) out of the four scaffolds are potential candidates for better anion recognition. By employing biophysical characterization using both qualitative and quantitative measures, in this present study, we report the interaction of sulfate and phosphate ions with these two designed scaffolds, in which there is much better recognition of anions by these scaffolds than the natural sequences, justifying their logical engineering. Our observation strongly suggests that these designed scaffolds are better potential candidates than those of the naturally occurring "CαNN" motif in terms of anion recognition and could be utilized for the scavenging of anion(s) for different purposes.
Collapse
Affiliation(s)
- Tridip Sheet
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
| | - Raja Banerjee
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
- Department
of Biotechnology, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
| |
Collapse
|
19
|
Abstract
How proteins evolved to recognize and bind their ligands is a key mystery in protein function evolution. To explore this mystery, we study how proteins bind adenine, an ancient fragment. We characterize physicochemical patterns of protein–adenine interactions and link these to proteins’ evolutionary origins. In conflict with previous findings, we see that all of adenine’s hydrogen donors and acceptors have been used to bind proteins, and that adenine binding is likely to have emerged multiple times in evolution. To identify adenine-binding sites of shared origin, we use “themes”: short amino acid segments suggested to constitute evolutionary building blocks. We detect specific themes that are engaged in adenine binding; the detection of these in a protein’s sequence might reveal its function. Proteins’ interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein–adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein–adenine interactions in the Watson–Crick edge of adenine and shows that all of adenine’s edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments (“themes”) that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
Collapse
|
20
|
Medvedev KE, Kinch LN, Schaeffer RD, Grishin NV. Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. PLoS Comput Biol 2019; 15:e1007569. [PMID: 31869345 PMCID: PMC6957218 DOI: 10.1371/journal.pcbi.1007569] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 01/13/2020] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Rossmann folds are ancient, frequently diverged domains found in many biological reaction pathways where they have adapted for different functions. Consequently, discernment and classification of their homologous relations and function can be complicated. We define a minimal Rossmann-like structure motif (RLM) that corresponds for the common core of known Rossmann domains and use this motif to identify all RLM domains in the Protein Data Bank (PDB), thus finding they constitute about 20% of all known 3D structures. The Evolutionary Classification of protein structure Domains (ECOD) classifies RLM domains in a number of groups that lack evidence for homology (X-groups), which suggests that they could have evolved independently multiple times. Closely related, homologous RLM enzyme families can diverge to bind different ligands using similar binding sites and to catalyze different reactions. Conversely, non-homologous RLM domains can converge to catalyze the same reactions or to bind the same ligand with alternate binding modes. We discuss a special case of such convergent evolution that is relevant to the polypharmacology paradigm, wherein the same drug (methotrexate) binds to multiple non-homologous RLM drug targets with different topologies. Finally, assigning proteins with RLM domain to the Enzyme Commission classification suggest that RLM enzymes function mainly in metabolism (and comprise 38% of reference metabolic pathways) and are overrepresented in extant pathways that represent ancient biosynthetic routes such as nucleotide metabolism, energy metabolism, and metabolism of amino acids. In fact, RLM enzymes take part in five out of eight enzymatic reactions of the Wood-Ljungdahl metabolic pathway thought to be used by the last universal common ancestor (LUCA). The prevalence of RLM domains in this ancient metabolism might explain their wide distribution among enzymes.
Collapse
Affiliation(s)
- Kirill E. Medvedev
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - R. Dustin Schaeffer
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| |
Collapse
|
21
|
Cong X, Yuan Z, Du Y, Wu B, Lu D, Wu X, Zhang Y, Li F, Wei B, Li J, Wu J, Xu S, Wang J, Qi J, Shang G, Gu L. Crystal structures of porcine STING CBD-CDN complexes reveal the mechanism of ligand recognition and discrimination of STING proteins. J Biol Chem 2019; 294:11420-11432. [PMID: 31167783 DOI: 10.1074/jbc.ra119.007367] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/02/2019] [Indexed: 01/11/2023] Open
Abstract
The cyclic dinucleotide (CDN)-stimulator of interferon genes (STING) pathway plays an important role in the detection of viral and bacterial pathogens in animals. Previous studies have shown that the metazoan second messenger cyclic [G(2',5')pA(3',5')p] (2',3'-cGAMP) generated by cyclic GMP-AMP synthase cGAS binds STING with high affinity compared with bacterial CDNs such as c-di-GMP, c-di-AMP, and 3',3'-cGAMP. Despite recent progress indicating that the CDN-binding domain (CBD) of dimeric STING binds asymmetric 2',3'-cGAMP preferentially over symmetric 3',3'-CDNs, it remains an open question whether STING molecules, such as human STING, adopt a symmetric dimeric conformation to efficiently engage its asymmetric ligand. Here, structural studies of the CBD from porcine STING (STINGCBD) in complex with CDNs at 1.76-2.6 Å resolution revealed that porcine STINGCBD, unlike its human and mouse counterparts, can adopt an asymmetric ligand-binding pocket to accommodate the CDNs. We observed that the extensive interactions and shape complementarity between asymmetric 2',3'-cGAMP and the ligand-binding pocket make it the most preferred ligand for porcine STING and that geometry constraints limit the binding between symmetric 3',3'-CDN and porcine STING. The ligand-discrimination mechanism of porcine STING observed here expands our understanding of how the CDN-STING pathway is activated and of its role in antiviral defense.
Collapse
Affiliation(s)
- Xiaoyan Cong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.,Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Yijun Du
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Bo Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230026, Anhui, China
| | - Defen Lu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Xiangju Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Youjia Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230026, Anhui, China
| | - Feng Li
- Department of Biology and Microbiology, Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota 57007
| | - Bin Wei
- Shandong Asia-Pacific Highharve Organisms Science and Technology Co., Ltd., No. 1 Jinneng Rd., Qihe, Shandong 251100, China
| | - Jun Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Jiaqiang Wu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Jinbao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Jing Qi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Sangyuan Rd. No. 8, Jinan 250100, China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
| |
Collapse
|
22
|
Parker MJ, Maggiolo AO, Thomas WC, Kim A, Meisburger SP, Ando N, Boal AK, Stubbe J. An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP. Proc Natl Acad Sci U S A 2018; 115:E4594-E4603. [PMID: 29712847 PMCID: PMC5960316 DOI: 10.1073/pnas.1800356115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme's quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2 dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner.
Collapse
Affiliation(s)
- Mackenzie J Parker
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ailiena O Maggiolo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - William C Thomas
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Albert Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ 08544;
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
23
|
Novel Metabolic Pathway for N-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1. Appl Environ Microbiol 2017; 84:AEM.02136-17. [PMID: 29030443 DOI: 10.1128/aem.02136-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
The molecular mechanisms underlying the biodegradation of N-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown. Alicycliphilus sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode an N-methylhydantoin amidohydrolase that transforms NMP to γ-N-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the nmp gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the nmpABCD genes. Similarly, Escherichia coli MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover, E. coli GABA-AT deletion mutants complemented with nmpABCD genes retained the ability to grow in NMP, supporting the possibility that γ-N-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.IMPORTANCEN-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for Alicycliphilus sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.
Collapse
|
24
|
Patra P, Ghosh M, Banerjee R, Chakrabarti J. Anion induced conformational preference of C α NN motif residues in functional proteins. Proteins 2017; 85:2179-2190. [PMID: 28905427 DOI: 10.1002/prot.25382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/16/2017] [Accepted: 09/10/2017] [Indexed: 11/12/2022]
Abstract
Among different ligand binding motifs, anion binding Cα NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with Cα NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping Cα NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.
Collapse
Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India.,The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector-III, Block JD, Salt Lake, Kolkata, 700106, India
| |
Collapse
|
25
|
Bhagavat R, Srinivasan N, Chandra N. Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites. Proteins 2017; 85:1699-1712. [PMID: 28547747 DOI: 10.1002/prot.25328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 12/14/2022]
Abstract
Nucleoside triphosphate (NTP) ligands are of high biological importance and are essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have used a structural bioinformatics approach and analyze structures of 4677 NTP complexes available in Protein Data Bank (PDB). Binding sites were extracted and compared exhaustively using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types. Each of these site-types represent a structural motif comprised of two or more residue conservations, derived using another in-house tool for superposing binding sites, PocketAlign. The 27 site-types could be grouped further into 9 super-types by considering partial similarities in the sites, which indicated that the individual site-types comprise different combinations of one or more site features. A scan across PDB using the 27 structural motifs determined the motifs to be specific to NTP binding sites, and a computational alanine mutagenesis indicated that residues identified to be highly conserved in the motifs are also most contributing to binding. Alternate orientations of the ligand in several site-types were observed and rationalized, indicating the possibility of some residues serving as anchors for NTP recognition. The presence of multiple site-types and the grouping of multiple folds into each site-type is strongly suggestive of convergent evolution. Knowledge of determinants obtained from this study will be useful for detecting function in unknown proteins. Proteins 2017; 85:1699-1712. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Raghu Bhagavat
- Department of Biochemistry, Molecular Biophysics Unit, National Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Narayanaswamy Srinivasan
- Department of Biochemistry, Molecular Biophysics Unit, National Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nagasuma Chandra
- Department of Biochemistry, Molecular Biophysics Unit, National Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| |
Collapse
|
26
|
Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1859-1871. [PMID: 28502790 DOI: 10.1016/j.bbamem.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 11/23/2022]
Abstract
Regulated intramembrane proteolysis by members of the site-2 protease family (S2P) is an essential signal transduction mechanism conserved from bacteria to humans. There is some evidence that extra-membranous domains, like PDZ and CBS domains, regulate the proteolytic activity of S2Ps and that some members act as dimers. Here we report the crystal structure of the regulatory CBS domain pair of S2P from Archaeoglobus fulgidus, AfS2P, in the apo and nucleotide-bound form in complex with a specific nanobody from llama. Cross-linking and SEC-MALS analyses show for the first time the dimeric architecture of AfS2P both in the membrane and in detergent micelles. The CBS domain pair dimer (CBS module) displays an unusual head-to-tail configuration and nucleotide binding triggers no major conformational changes in the magnesium-free state. In solution, MgATP drives monomerization of the CBS module. We propose a model of the so far unknown architecture of the transmembrane domain dimer and for a regulatory mechanism of AfS2P that involves the interaction of positively charged arginine residues located at the cytoplasmic face of the transmembrane domain with the negatively charged phosphate groups of ATP moieties bound to the CBS domain pairs. Binding of MgATP could promote opening of the CBS module to allow lateral access of the globular cytoplasmic part of the substrate.
Collapse
|
27
|
Cahn JKB, Werlang CA, Baumschlager A, Brinkmann-Chen S, Mayo SL, Arnold FH. A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases. ACS Synth Biol 2017; 6:326-333. [PMID: 27648601 DOI: 10.1021/acssynbio.6b00188] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to control enzymatic nicotinamide cofactor utilization is critical for engineering efficient metabolic pathways. However, the complex interactions that determine cofactor-binding preference render this engineering particularly challenging. Physics-based models have been insufficiently accurate and blind directed evolution methods too inefficient to be widely adopted. Building on a comprehensive survey of previous studies and our own prior engineering successes, we present a structure-guided, semirational strategy for reversing enzymatic nicotinamide cofactor specificity. This heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. We demonstrate the efficacy of this strategy by inverting the cofactor specificity of four structurally diverse NADP-dependent enzymes: glyoxylate reductase, cinnamyl alcohol dehydrogenase, xylose reductase, and iron-containing alcohol dehydrogenase. The analytical components of this approach have been fully automated and are available in the form of an easy-to-use web tool: Cofactor Specificity Reversal-Structural Analysis and Library Design (CSR-SALAD).
Collapse
Affiliation(s)
- Jackson K. B. Cahn
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Caroline A. Werlang
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Armin Baumschlager
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Stephen L. Mayo
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, and ‡Division of Biology and Biological
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
28
|
Doig AJ. Frozen, but no accident – why the 20 standard amino acids were selected. FEBS J 2017; 284:1296-1305. [DOI: 10.1111/febs.13982] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Doig
- Department of Chemistry Manchester Institute of Biotechnology University of Manchester UK
| |
Collapse
|
29
|
He W, Liang Z, Teng M, Niu L. LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition. FEBS Open Bio 2016; 6:1331-1340. [PMID: 28255540 PMCID: PMC5324770 DOI: 10.1002/2211-5463.12150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/23/2022] Open
Abstract
Identifying conserved binding motifs is an efficient way to study protein–ligand recognition. Most 3D binding motifs only contain information from the protein side, and so motifs that combine information from both protein and ligand sides are desired. Here, we propose an algorithm called LibME (Ligand‐binding Motif Extractor), which automatically extracts 3D binding motifs composed of the target ligand and surrounding conserved residues. We show that the motifs extracted by LibME for ATP and its analogs are highly similar to well‐known motifs reported by previous studies. The superiority of our method to handle flexible ligands was also demonstrated using isocitric acid as an example. Finally, we show that these motifs, together with their visual exhibition, permit better investigating and understanding of protein–ligand recognition process.
Collapse
Affiliation(s)
- Wei He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - Zhi Liang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - MaiKun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| | - LiWen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences University of Science and Technology of China Anhui China
| |
Collapse
|
30
|
Kiese K, Jablonski J, Boison D, Kobow K. Dynamic Regulation of the Adenosine Kinase Gene during Early Postnatal Brain Development and Maturation. Front Mol Neurosci 2016; 9:99. [PMID: 27812320 PMCID: PMC5071315 DOI: 10.3389/fnmol.2016.00099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/26/2016] [Indexed: 12/02/2022] Open
Abstract
The ubiquitous metabolic intermediary and nucleoside adenosine is a “master regulator” in all living systems. Under baseline conditions adenosine kinase (ADK) is the primary enzyme for the metabolic clearance of adenosine. By regulating the availability of adenosine, ADK is a critical upstream regulator of complex homeostatic and metabolic networks. Not surprisingly, ADK dysfunction is involved in several pathologies, including diabetes, epilepsy, and cancer. ADK protein exists in the two isoforms nuclear ADK-L, and cytoplasmic ADK-S, which are subject to dynamic expression changes during brain development and in response to brain injury; however, gene expression changes of the Adk gene as well as regulatory mechanisms that direct the cell-type and isoform specific expression of ADK have never been investigated. Here we analyzed potential gene regulatory mechanisms that may influence Adk expression including DNA promoter methylation, histone modifications and transcription factor binding. Our data suggest binding of transcription factor SP1 to the Adk promoter influences the regulation of Adk expression.
Collapse
Affiliation(s)
- Katharina Kiese
- Department of Neuropathology, University Hospital Erlangen Erlangen, Germany
| | - Janos Jablonski
- Department of Neuropathology, University Hospital Erlangen Erlangen, Germany
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute Portland, OR, USA
| | - Katja Kobow
- Department of Neuropathology, University Hospital Erlangen Erlangen, Germany
| |
Collapse
|
31
|
Kasahara K, Kinoshita K. Landscape of protein-small ligand binding modes. Protein Sci 2016; 25:1659-71. [PMID: 27327045 PMCID: PMC5338237 DOI: 10.1002/pro.2971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 06/04/2016] [Accepted: 06/15/2016] [Indexed: 11/15/2022]
Abstract
Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2) = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.
Collapse
Affiliation(s)
- Kota Kasahara
- College of Life SciencesRitsumeikan UniversityKusatsuShiga525‐8577Japan
| | - Kengo Kinoshita
- Graduate School of Information SciencesTohoku UniversitySendaiMiyagi980‐8597Japan
- Tohoku Medical Megabank OrganizationTohoku UniversitySendaiMiyagi980‐8573Japan
- Institute of Development, Aging and Cancer, Tohoku UniversitySendaiMiyagi980‐8575Japan
| |
Collapse
|
32
|
Choi KY. Non-enzymatic PLP-dependent oxidative deamination of amino acids induces higher alcohol synthesis. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0434-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
33
|
Zheng Z, Goncearenco A, Berezovsky IN. Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions. Nucleic Acids Res 2015; 44:D301-7. [PMID: 26507856 PMCID: PMC4702817 DOI: 10.1093/nar/gkv1124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/14/2015] [Indexed: 11/14/2022] Open
Abstract
NBDB database describes protein motifs, elementary functional loops (EFLs) that are involved in binding of nucleotide-containing ligands and other biologically relevant cofactors/coenzymes, including ATP, AMP, ATP, GMP, GDP, GTP, CTP, PAP, PPS, FMN, FAD(H), NAD(H), NADP, cAMP, cGMP, c-di-AMP and c-di-GMP, ThPP, THD, F-420, ACO, CoA, PLP and SAM. The database is freely available online at http://nbdb.bii.a-star.edu.sg. In total, NBDB contains data on 249 motifs that work in interactions with 24 ligands. Sequence profiles of EFL motifs were derived de novo from nonredundant Uniprot proteome sequences. Conserved amino acid residues in the profiles interact specifically with distinct chemical parts of nucleotide-containing ligands, such as nitrogenous bases, phosphate groups, ribose, nicotinamide, and flavin moieties. Each EFL profile in the database is characterized by a pattern of corresponding ligand–protein interactions found in crystallized ligand–protein complexes. NBDB database helps to explore the determinants of nucleotide and cofactor binding in different protein folds and families. NBDB can also detect fragments that match to profiles of particular EFLs in the protein sequence provided by user. Comprehensive information on sequence, structures, and interactions of EFLs with ligands provides a foundation for experimental and computational efforts on design of required protein functions.
Collapse
Affiliation(s)
- Zejun Zheng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | | | - Igor N Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore
| |
Collapse
|
34
|
Chen K, Wang D, Kurgan L. Systematic investigation of sequence and structural motifs that recognize ATP. Comput Biol Chem 2015; 56:131-41. [PMID: 25935117 DOI: 10.1016/j.compbiolchem.2015.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/05/2015] [Accepted: 04/18/2015] [Indexed: 02/07/2023]
Abstract
Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP-protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP.
Collapse
Affiliation(s)
- Ke Chen
- School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin 300387, China.
| | - Dacheng Wang
- School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin 300387, China
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, 2nd floor, ECERF (9107 116 Street), University of Alberta, Edmonton, AB T6G 2V4, Canada
| |
Collapse
|
35
|
Kuppuraj G, Kruise D, Yura K. Conformational behavior of flavin adenine dinucleotide: conserved stereochemistry in bound and free states. J Phys Chem B 2014; 118:13486-97. [PMID: 25389798 DOI: 10.1021/jp507629n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metabolic enzymes utilize the cofactor flavin adenine dinucleotide (FAD) to catalyze essential biochemical reactions. Because these enzymes have been implicated in disease pathways, it will be necessary to target them via FAD-based structural analogues that can either activate/inhibit the enzymatic activity. To achieve this, it is important to explore the conformational space of FAD in the enzyme-bound and free states. Herein, we analyze X-ray crystallographic data of the enzyme-bound FAD conformations and sample conformations of the molecule in explicit water by molecular dynamics (MD) simulations. Enzyme-bound FAD conformations segregate into five distinct groups based on dihedral angle principal component analysis (PCA). A notable feature in the bound FADs is that the adenine base and isoalloxazine ring are oppositely oriented relative to the pyrophosphate axis characterized by near trans hypothetical dihedral angle "δV" values. Not surprisingly, MD simulations in water show final compact but not perfectly stacked ring structures in FAD. Simulation data did not reveal noticeable changes in overall conformational dynamics of the dinucleotide in reduced and oxidized forms and in the presence and/or absence of ions. During unfolding-folding dynamics, the riboflavin moiety is more flexible than the adenosine monophosphate group in the molecule. Conversely, the isoalloxazine ring is more stable than the variable adenine base. The pyrophosphate group depicts an unusually highly organized fluctuation illustrated by its dihedral angle distribution. Conformations sampled from enzymes and MD are quantified. The extent to which the protein shifts the distribution from the unbound state is discussed in terms of prevalent FAD shapes and dihedral angle population.
Collapse
Affiliation(s)
- Gopi Kuppuraj
- Center for Informational Biology, Ochanomizu University , 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | | | | |
Collapse
|
36
|
Zhu X, Xiong Y, Kihara D. Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. ACTA ACUST UNITED AC 2014; 31:707-13. [PMID: 25359888 DOI: 10.1093/bioinformatics/btu724] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects. RESULTS We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods. AVAILABILITY AND IMPLEMENTATION http://kiharalab.org/patchsurfer2.0/ CONTACT: dkihara@purdue.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Xiaolei Zhu
- Department of Biological Science, Purdue University, West Lafayette, IN 47906, USA and Department of Computer Science, Purdue University, West Lafayette, IN 47906, USA
| | - Yi Xiong
- Department of Biological Science, Purdue University, West Lafayette, IN 47906, USA and Department of Computer Science, Purdue University, West Lafayette, IN 47906, USA
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, IN 47906, USA and Department of Computer Science, Purdue University, West Lafayette, IN 47906, USA Department of Biological Science, Purdue University, West Lafayette, IN 47906, USA and Department of Computer Science, Purdue University, West Lafayette, IN 47906, USA
| |
Collapse
|
37
|
Westermaier Y, Barril X, Scapozza L. Virtual screening: an in silico tool for interlacing the chemical universe with the proteome. Methods 2014; 71:44-57. [PMID: 25193260 DOI: 10.1016/j.ymeth.2014.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/16/2014] [Accepted: 08/02/2014] [Indexed: 12/28/2022] Open
Abstract
In silico screening both in the forward (traditional virtual screening) and reverse sense (inverse virtual screening (IVS)) are helpful techniques for interlacing the chemical universe of small molecules with the proteome. The former, which is using a protein structure and a large chemical database, is well-known by the scientific community. We have chosen here to provide an overview on the latter, focusing on validation and target prioritization strategies. By comparing it to complementary or alternative wet-lab approaches, we put IVS in the broader context of chemical genomics, target discovery and drug design. By giving examples from the literature and an own example on how to validate the approach, we provide guidance on the issues related to IVS.
Collapse
Affiliation(s)
- Yvonne Westermaier
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland; Computational Biology & Drug Design Group, Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Xavier Barril
- Computational Biology & Drug Design Group, Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland.
| |
Collapse
|
38
|
Egel R. Origins and emergent evolution of life: the colloid microsphere hypothesis revisited. ORIGINS LIFE EVOL B 2014; 44:87-110. [PMID: 25208738 DOI: 10.1007/s11084-014-9363-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 08/14/2014] [Indexed: 11/28/2022]
Abstract
Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life's complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative 'protolife' communities, in which 'protoplasmic continuity' was maintained throughout a graded series of 'proto-biofilms', 'protoorganisms' and 'protocells' toward modern life. The proneness of organic microspheres to merge back into the bulk of sessile films by spontaneous fusion can have made large populations promiscuous from the beginning, which was important for the speed of collective evolution early on. In this protein-centered scenario, the emergent coevolution of uncoded peptides, metabolic cofactors and oligoribonucleotides was primarily optimized for system-supporting catalytic capabilities arising from nonribosomal peptide synthesis and nonreplicative ribonucleotide polymerization, which in turn incorporated other reactive micromolecular organics as vitamins and cofactors into composite macromolecular colloid films and microspheres. Template-dependent replication and gene-encoded protein synthesis emerged as secondary means for further optimization of overall efficieny later on. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms.
Collapse
Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200, Copenhagen, Denmark,
| |
Collapse
|
39
|
Mugo AN, Kobayashi J, Yamasaki T, Mikami B, Ohnishi K, Yoshikane Y, Yagi T. Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:953-63. [PMID: 23501672 DOI: 10.1016/j.bbapap.2013.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
Abstract
Pyridoxine 4-oxidase (PNOX) from Mesorhizobium loti is a monomeric glucose-methanol-choline (GMC) oxidoreductase family enzyme, catalyzes FAD-dependent oxidation of pyridoxine (PN) into pyridoxal, and is the first enzyme in pathway I for the degradation of PN. The tertiary structures of PNOX with a C-terminal His6-tag and PNOX-pyridoxamine (PM) complex were determined at 2.2Å and at 2.1Å resolutions, respectively. The overall structure consisted of FAD-binding and substrate-binding domains. In the active site, His460, His462, and Pro504 were located on the re-face of the isoalloxazine ring of FAD. PM binds to the active site through several hydrogen bonds. The side chains of His462 and His460 are located at 2.7 and 3.1Å from the N4' atom of PM. The activities of His460Ala and His462Ala mutant PNOXs were very low, and 460Ala/His462Ala double mutant PNOX exhibited no activity. His462 may act as a general base for the abstraction of a proton from the 4'-hydroxyl of PN. His460 may play a role in the binding and positioning of PN. The C4' atom in PM is located at 3.2Å, and the hydride ion from the C4' atom may be transferred to the N5 atom of the isoalloxazine ring. The comparison of active site residues in GMC oxidoreductase shows that Pro504 in PNOX corresponds to Asn or His of the conserved His-Asn or His-His pair in other GMC oxidoreductases. The function of the novel proline residue was discussed.
Collapse
Affiliation(s)
- Andrew Njagi Mugo
- Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi, Japan
| | | | | | | | | | | | | |
Collapse
|
40
|
Sheet T, Supakar S, Banerjee R. Conformational preference of 'CαNN' short peptide motif towards recognition of anions. PLoS One 2013; 8:e57366. [PMID: 23516403 PMCID: PMC3596363 DOI: 10.1371/journal.pone.0057366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction.
Collapse
Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Subhrangshu Supakar
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Raja Banerjee
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
- * E-mail:
| |
Collapse
|
41
|
Kalliokoski T, Olsson TSG, Vulpetti A. Subpocket analysis method for fragment-based drug discovery. J Chem Inf Model 2013; 53:131-41. [PMID: 23327721 DOI: 10.1021/ci300523r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Although two binding sites might be dissimilar overall, they might still bind the same fragments if they share suitable subpockets. Information about shared subpockets can be therefore used in fragment-based drug design to suggest new fragments or to replace existing fragments within an already known compound. A novel computational method called SubCav is described which allows the similarity searching and alignment of subpockets from a PDB-wide database against a user-defined query. The method is based on pharmacophoric fingerprints combined with a subpocket alignment algorithm. SubCav was shown to be effective in producing reasonable alignments for subpockets with low sequence similarity and be able to retrieve relevant subpockets from a large database of structures including those with different folds. It can also be used to analyze subpockets inside a protein family to facilitate drug design and to rationalize compound selectivity.
Collapse
Affiliation(s)
- Tuomo Kalliokoski
- Novartis Institutes for Biomedical Research, Postfach, CH-4002 Basel, Switzerland
| | | | | |
Collapse
|
42
|
Lee HS, Im W. Identification of ligand templates using local structure alignment for structure-based drug design. J Chem Inf Model 2012; 52:2784-95. [PMID: 22978550 DOI: 10.1021/ci300178e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.
Collapse
Affiliation(s)
- Hui Sun Lee
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA.
| | | |
Collapse
|
43
|
The phylogenomic roots of modern biochemistry: origins of proteins, cofactors and protein biosynthesis. J Mol Evol 2012; 74:1-34. [PMID: 22210458 DOI: 10.1007/s00239-011-9480-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 12/12/2011] [Indexed: 12/20/2022]
Abstract
The complexity of modern biochemistry developed gradually on early Earth as new molecules and structures populated the emerging cellular systems. Here, we generate a historical account of the gradual discovery of primordial proteins, cofactors, and molecular functions using phylogenomic information in the sequence of 420 genomes. We focus on structural and functional annotations of the 54 most ancient protein domains. We show how primordial functions are linked to folded structures and how their interaction with cofactors expanded the functional repertoire. We also reveal protocell membranes played a crucial role in early protein evolution and show translation started with RNA and thioester cofactor-mediated aminoacylation. Our findings allow elaboration of an evolutionary model of early biochemistry that is firmly grounded in phylogenomic information and biochemical, biophysical, and structural knowledge. The model describes how primordial α-helical bundles stabilized membranes, how these were decorated by layered arrangements of β-sheets and α-helices, and how these arrangements became globular. Ancient forms of aminoacyl-tRNA synthetase (aaRS) catalytic domains and ancient non-ribosomal protein synthetase (NRPS) modules gave rise to primordial protein synthesis and the ability to generate a code for specificity in their active sites. These structures diversified producing cofactor-binding molecular switches and barrel structures. Accretion of domains and molecules gave rise to modern aaRSs, NRPS, and ribosomal ensembles, first organized around novel emerging cofactors (tRNA and carrier proteins) and then more complex cofactor structures (rRNA). The model explains how the generation of protein structures acted as scaffold for nucleic acids and resulted in crystallization of modern translation.
Collapse
|
44
|
Tadwal VS, Manimekalai MSS, Grüber G. Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1485-91. [PMID: 22139149 PMCID: PMC3232122 DOI: 10.1107/s1744309111039595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
A reporter tryptophan residue was individually introduced by site-directed mutagenesis into the adenine-binding pocket of the catalytic subunit A (F427W and F508W mutants) of the motor protein A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3. The crystal structures of the F427W and F508W mutant proteins were determined to 2.5 and 2.6 Å resolution, respectively. The tryptophan substitution caused the fluorescence signal to increase by 28% (F427W) and 33% (F508W), with a shift from 333 nm in the wild-type protein to 339 nm in the mutant proteins. Tryptophan emission spectra showed binding of Mg-ATP to the F427W mutant with a K(d) of 8.5 µM. In contrast, no significant binding of nucleotide could be observed for the F508W mutant. A closer inspection of the crystal structure of the F427W mutant showed that the adenine-binding pocket had widened by 0.7 Å (to 8.70 Å) in comparison to the wild-type subunit A (8.07 Å) owing to tryptophan substitution, as a result of which it was able to bind ATP. In contrast, the adenine-binding pocket had narrowed in the F508W mutant. The two mutants presented demonstrate that the exact volume of the adenine ribose binding pocket is essential for nucleotide binding and even minor narrowing makes it unfit for nucleotide binding. In addition, structural and fluorescence data confirmed the viability of the fluorescently active mutant F427W, which had ideal tryptophan spectra for future structure-based time-resolved dynamic measurements of the catalytic subunit A of the ATP-synthesizing enzyme A-ATP synthase.
Collapse
|
45
|
Rantanen VV, Gyllenberg M, Koski T, Johnson MS. A PRIORI CONTACT PREFERENCES IN MOLECULAR RECOGNITION. J Bioinform Comput Biol 2011; 3:861-90. [PMID: 16078365 DOI: 10.1142/s0219720005001417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 11/29/2004] [Indexed: 11/18/2022]
Abstract
A molecular interaction library modeling favorable non-bonded interactions between atoms and molecular fragments is considered. In this paper, we represent the structure of the interaction library by a network diagram, which demonstrates that the underlying prediction model obtained for a molecular fragment is multi-layered. We clustered the molecular fragments into four groups by analyzing the pairwise distances between the molecular fragments. The distances are represented as an unrooted tree, in which the molecular fragments fall into four groups according to their function. For each fragment group, we modeled a group-specific a priori distribution with a Dirichlet distribution. The group-specific Dirichlet distributions enable us to derive a large population of similar molecular fragments that vary only in their contact preferences. Bayes' theorem then leads to a population distribution of the posterior probability vectors referred to as a "Dickey–Savage"-density. Two known methods for approximating multivariate integrals are applied to obtain marginal distributions of the Dickey–Savage density. The results of the numerical integration methods are compared with the simulated marginal distributions. By studying interactions between the protein structure of cyclohydrolase and its ligand guanosine-5′-triphosphate, we show that the marginal distributions of the posterior probabilities are more informative than the corresponding point estimates.
Collapse
|
46
|
Kondabagil K, Draper B, Rao VB. Adenine recognition is a key checkpoint in the energy release mechanism of phage T4 DNA packaging motor. J Mol Biol 2011; 415:329-42. [PMID: 22100308 DOI: 10.1016/j.jmb.2011.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 11/25/2022]
Abstract
ATP is the source of energy for numerous biochemical reactions in all organisms. Tailed bacteriophages use ATP to drive powerful packaging machines that translocate viral DNA into a procapsid and compact it to near-crystalline density. Here we report that a complex network of interactions dictates adenine recognition and ATP hydrolysis in the pentameric phage T4 large "terminase" (gp17) motor. The network includes residues that form hydrogen bonds at the edges of the adenine ring (Q138 and Q143), base-stacking interactions at the plane of the ring (I127 and R140), and cross-talking bonds between adenine, triphosphate, and Walker A P-loop (Y142, Q143, and R140). These interactions are conserved in other translocases such as type I/type III restriction enzymes and SF1/SF2 helicases. Perturbation of any of these interactions, even the loss of a single hydrogen bond, leads to multiple defects in motor functions. Adenine recognition is therefore a key checkpoint that ensures efficient ATP firing only when the fuel molecule is precisely engaged with the motor. This may be a common feature in the energy release mechanism of ATP-driven molecular machines that carry out numerous biomolecular reactions in biological systems.
Collapse
Affiliation(s)
- Kiran Kondabagil
- Department of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC 20064, USA
| | | | | |
Collapse
|
47
|
Kondo J, Westhof E. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes. Nucleic Acids Res 2011; 39:8628-37. [PMID: 21737431 PMCID: PMC3201857 DOI: 10.1093/nar/gkr452] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.
Collapse
Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan.
| | | |
Collapse
|
48
|
Zhang Z, Zhou R, Sauder JM, Tonge PJ, Burley SK, Swaminathan S. Structural and functional studies of fatty acyl adenylate ligases from E. coli and L. pneumophila. J Mol Biol 2010; 406:313-24. [PMID: 21185305 DOI: 10.1016/j.jmb.2010.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 11/29/2010] [Accepted: 12/05/2010] [Indexed: 11/15/2022]
Abstract
Fatty acyl-AMP ligase (FAAL) is a new member of a family of adenylate-forming enzymes that were recently discovered in Mycobacterium tuberculosis. They are similar in sequence to fatty acyl-coenzyme A (CoA) ligases (FACLs). However, while FACLs perform a two-step catalytic reaction, AMP ligation followed by CoA ligation using ATP and CoA as cofactors, FAALs produce only the acyl adenylate and are unable to perform the second step. We report X-ray crystal structures of full-length FAAL from Escherichia coli (EcFAAL) and FAAL from Legionella pneumophila (LpFAAL) bound to acyl adenylate, determined at resolution limits of 3.0 and 1.85 Å, respectively. The structures share a larger N-terminal domain and a smaller C-terminal domain, which together resemble the previously determined structures of FAAL and FACL proteins. Our two structures occur in quite different conformations. EcFAAL adopts the adenylate-forming conformation typical of FACLs, whereas LpFAAL exhibits a unique intermediate conformation. Both EcFAAL and LpFAAL have insertion motifs that distinguish them from the FACLs. Structures of EcFAAL and LpFAAL reveal detailed interactions between this insertion motif and the interdomain hinge region and with the C-terminal domain. We suggest that the insertion motifs support sufficient interdomain motions to allow substrate binding and product release during acyl adenylate formation, but they preclude CoA binding, thereby preventing CoA ligation.
Collapse
Affiliation(s)
- Zhening Zhang
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | | | | | | | | |
Collapse
|
49
|
Pyrkov TV, Ozerov IV, Blitskaia ED, Efremov RG. [Molecular docking: role of intermolecular contacts in formation of complexes of proteins with nucleotides and peptides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:482-92. [PMID: 20823916 DOI: 10.1134/s1068162010040023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of 3D-structure of protein-ligand complex is a major prerequisite for understanding the functioning mechanism of cellular proteins and membrane receptors. This is also of a great help in rational drug design projects. In the present paper we briefly review the molecular docking approaches used to predict possible orientation of a ligand in the protein binding site. The recent trends to improve the accuracy and efficiency of docking algorithms are demonstrated with the results obtained in Laboratory of Biomolecular Modeling. Particular attention is paid to protein-ligand hydrophobic and stacking interactions responsible for molecular recognition of ligand fragments. Such type of interactions are not always adequately represented in scoring criteria of docking applications that leads to mismatch in 3D-structure complexes predictions. That is why further inquiry of methods to account for these interactions is now the area of active research.
Collapse
|
50
|
Simmons CR, Magee CL, Smith DA, Lauman L, Chaput JC, Allen JP. Three-dimensional structures reveal multiple ADP/ATP binding modes for a synthetic class of artificial proteins. Biochemistry 2010; 49:8689-99. [PMID: 20822107 DOI: 10.1021/bi100398p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.
Collapse
Affiliation(s)
- C R Simmons
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | | | | | | | | | | |
Collapse
|