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Jacobs FJ, Helliwell JR, Brink A. Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development. IUCRJ 2024; 11:359-373. [PMID: 38639558 PMCID: PMC11067751 DOI: 10.1107/s2052252524002598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.
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Affiliation(s)
- Francois J.F. Jacobs
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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2
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Kumar YB, Kumar N, John L, Mahanta HJ, Vaikundamani S, Nagamani S, Sastry GM, Sastry GN. Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0. Proteins 2024; 92:179-191. [PMID: 37789571 DOI: 10.1002/prot.26600] [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: 06/22/2023] [Revised: 08/17/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Lijo John
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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3
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Kumar YB, Kumar N, Vaikundamani S, Nagamani S, Mahanta HJ, Sastry GM, Sastry GN. Analyzing the aromatic-aromatic interactions in proteins: A 2ID 2.0. Int J Biol Macromol 2023; 253:127207. [PMID: 37797858 DOI: 10.1016/j.ijbiomac.2023.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/09/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023]
Abstract
The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.
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Affiliation(s)
- Y Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India
| | - G Madhavi Sastry
- Schrödinger Inc., HITEC City, Hyderabad, Telangana 500081, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India.
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4
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The Structure of Evolutionary Model Space for Proteins across the Tree of Life. BIOLOGY 2023; 12:biology12020282. [PMID: 36829559 PMCID: PMC9952988 DOI: 10.3390/biology12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The factors that determine the relative rates of amino acid substitution during protein evolution are complex and known to vary among taxa. We estimated relative exchangeabilities for pairs of amino acids from clades spread across the tree of life and assessed the historical signal in the distances among these clade-specific models. We separately trained these models on collections of arbitrarily selected protein alignments and on ribosomal protein alignments. In both cases, we found a clear separation between the models trained using multiple sequence alignments from bacterial clades and the models trained on archaeal and eukaryotic data. We assessed the predictive power of our novel clade-specific models of sequence evolution by asking whether fit to the models could be used to identify the source of multiple sequence alignments. Model fit was generally able to correctly classify protein alignments at the level of domain (bacterial versus archaeal), but the accuracy of classification at finer scales was much lower. The only exceptions to this were the relatively high classification accuracy for two archaeal lineages: Halobacteriaceae and Thermoprotei. Genomic GC content had a modest impact on relative exchangeabilities despite having a large impact on amino acid frequencies. Relative exchangeabilities involving aromatic residues exhibited the largest differences among models. There were a small number of exchangeabilities that exhibited large differences in comparisons among major clades and between generalized models and ribosomal protein models. Taken as a whole, these results reveal that a small number of relative exchangeabilities are responsible for much of the structure of the "model space" for protein sequence evolution. The clade-specific models we generated may be useful tools for protein phylogenetics, and the structure of evolutionary model space that they revealed has implications for phylogenomic inference across the tree of life.
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Kumar YB, Pandey A, Kumar N, Sastry GN. Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study. J Comput Chem 2023; 44:432-441. [PMID: 36583416 DOI: 10.1002/jcc.26977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 01/03/2023]
Abstract
Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.
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Affiliation(s)
- Yenamareddy Bhargav Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anwesh Pandey
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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6
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Crystal structures of FNIP/FGxxFN motif-containing leucine-rich repeat proteins. Sci Rep 2022; 12:16430. [PMID: 36180492 PMCID: PMC9525666 DOI: 10.1038/s41598-022-20758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/19/2022] [Indexed: 11/14/2022] Open
Abstract
The Cafeteria roenbergensis virus (Crov), Dictyostelium, and other species encode a large family of leucine-rich repeat (LRR) proteins with FGxxFN motifs. We determined the structures of two of them and observed several unique structural features that set them aside from previously characterized LRR family members. Crov588 comprises 25 regular repeats with a LxxLxFGxxFNQxIxENVLPxx consensus, forming a unique closed circular repeat structure. Novel features include a repositioning of a conserved asparagine at the middle of the repeat, a double phenylalanine spine that generates an alternate core packing arrangement, and a histidine/tyrosine ladder on the concave surface. Crov539 is smaller, comprising 12 repeats of a similar LxxLxFGxxFNQPIExVxW/LPxx consensus and forming an unusual cap-swapped dimer structure. The phenylalanine spine of Crov539 is supplemented with a tryptophan spine, while a hydrophobic isoleucine-rich patch is found on the central concave surface. We present a detailed analysis of the structures of Crov588 and Crov539 and compare them to related repeat proteins and other LRR classes.
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7
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Umar S, Singh AK, Chourasia M, Rasmussen SM, Ruth JH, Ahmed S. Penta-o-galloyl-beta-d-Glucose (PGG) inhibits inflammation in human rheumatoid arthritis synovial fibroblasts and rat adjuvant-induced arthritis model. Front Immunol 2022; 13:928436. [PMID: 36032089 PMCID: PMC9400595 DOI: 10.3389/fimmu.2022.928436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
O-GlcNAcylation is a reversible post-translational modification that regulates numerous cellular processes, including embryonic development as well as immune responses. However, its role in inflammation remains ambiguous. This study was designed to examine the role of O-GlcNAcylation in rheumatoid arthritis (RA) and its regulation using human RA patient-derived synovial fibroblasts (RASFs). The efficacy of penta-O-galloyl-beta-D-glucose (PGG), a potent anti-inflammatory molecule, in regulating inflammatory processes in human RASFs was also evaluated. Human synovial tissues and RASFs exhibited higher expression of O-GlcNAcylation compared to their non-diseased counterparts. Pretreatment of RASFs with Thiamet G, an inhibitor of O-GlcNAcase, markedly increased the O-GlcNAc-modified proteins and concomitantly inhibited the IL-1β-induced IL-6 and IL-8 production in human RASFs in vitro. Pretreatment of human RASFs with PGG (0.5-10 µM) abrogated IL-1β-induced IL-6 and IL-8 production in a dose-dependent manner. Immunoprecipitation analysis showed that PGG inhibited O-GlcNAcylation of TAB1 to reduce its association with TGF β-activated kinase 1 (TAK1) and its autophosphorylation, an essential signaling step in IL-1β-induced signaling pathways. Molecular docking in silico studies shows that PGG occupies the C174 position, an ATP-binding site in the kinase domain to inhibit TAK1 kinase activity. Oral administration of PGG (25 mg/kg/day) for 10 days from disease onset significantly ameliorated rat adjuvant-induced (AIA) in rats. PGG treatment reduced the phosphorylation of TAK1 in the treated joints compared to AIA joints, which correlated with the reduced disease severity and suppressed levels of serum IL-1β, GM-CSF, TNF-α, and RANKL. These findings suggest O-GlcNAcylation as a potential therapeutic target and provide the rationale for testing PGG or structurally similar molecule for their therapeutic efficacy.
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Affiliation(s)
- Sadiq Umar
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Anil K. Singh
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
| | - Mukesh Chourasia
- Center for Computational Biology and Bioinformatics, Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Stephanie M. Rasmussen
- Division of Rheumatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jeffrey H. Ruth
- Division of Rheumatology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Salahuddin Ahmed
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy and Pharmaceutical Sciences, Spokane, WA, United States
- Division of Rheumatology, University of Washington School of Medicine, Seattle, WA, United States
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8
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PIF - A Java library for finding atomic interactions and extracting geometric features supporting the analysis of protein structures. Methods 2022; 205:63-72. [PMID: 35724844 DOI: 10.1016/j.ymeth.2022.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/13/2022] [Accepted: 04/16/2022] [Indexed: 11/22/2022] Open
Abstract
Proteins play an essential role in the functioning of living organisms. The enormity of the atomic interactions in proteins is essential in controlling their spatial structures and dynamics. It can also provide scientists with valuable information that help to determine the native structures of proteins. This paper presents the PIF (Protein Interaction Finder) library for the Java language, enabling the identification of selected atomic interactions (hydrogen and disulfide bonds, ionic, hydrophobic, aromatic-aromatic, sulfur-aromatic, and amino-aromatic interactions) based on the three-dimensional structure of proteins. The interaction calculation rules applied in PIF rely on documented theoretical foundations gathered from experimental studies of interactions in native protein structures. The library has a universal purpose, supporting drug discovery and development processes and protein structure modeling. Finding the atomic interactions can also deliver numerical features for various Artificial Intelligence (AI) models built for protein analysis. The conducted research comparing the results obtained with the use of the PIF library and competing tools has shown that our solution can effectively determine the interactions occurring in protein structures for entire collections of proteins. Moreover, as a solution that provides a programming interface, the PIF library can be used in any Java project, making it a universal tool.
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Jian J, Barkhatova D, Hammink R, Tinnemans P, Bickelhaupt FM, Poater J, Mecinović J. Through-Space Stabilization of an Imidazolium Cation by Aromatic Rings. J Org Chem 2022; 87:7875-7883. [PMID: 35653132 DOI: 10.1021/acs.joc.2c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Imidazole-based compounds are widely found in natural products, synthetic molecules, and biomolecules. Noncovalent interactions between the imidazole ring and other functional groups play an important role in determining the function of diverse molecules. However, there is a limited understanding of the underlying noncovalent interactions between imidazoles and aromatic systems. In this work, we report physical-organic chemistry studies on 2-(2,6-diarylphenyl)-1H-imidazoles and their protonated forms to investigate the noncovalent interactions between the central imidazole ring and two flanking aromatic rings possessing substituents at the para/meta position. Hammett analysis revealed that pKa values and proton affinities correlate well with Hammett σ values of para-substituents at the flanking rings. Additional quantitative Kohn-Sham molecular orbital and energy decomposition analyses reveal that through-space π-π interactions and NH-π interactions contribute to the intramolecular stabilization of the imidazolium cation. The results are important because they clearly demonstrate that the imidazolium cation forms energetically favorable noncovalent interactions with aromatic rings via the through-space effect, a knowledge that can be used in rational drug and catalyst design.
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Affiliation(s)
- Jie Jian
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Darina Barkhatova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Roel Hammink
- Division of Immunotherapy, Oncode Institute, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands.,Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 26, 6525 GA Nijmegen, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - F Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jordi Poater
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.,Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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Patarroyo MA, Patarroyo ME, Pabón L, Alba MP, Bermudez A, Rugeles MT, Díaz-Arevalo D, Zapata-Builes W, Zapata MI, Reyes C, Suarez CF, Agudelo W, López C, Aza-Conde J, Melo M, Escamilla L, Oviedo J, Guzmán F, Silva Y, Forero M, Flórez-Álvarez L, Aguilar-Jimenez W, Moreno-Vranich A, Garry J, Avendaño C. SM-COLSARSPROT: Highly Immunogenic Supramutational Synthetic Peptides Covering the World's Population. Front Immunol 2022; 13:859905. [PMID: 35693819 PMCID: PMC9175637 DOI: 10.3389/fimmu.2022.859905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Fifty ~20-amino acid (aa)-long peptides were selected from functionally relevant SARS-CoV-2 S, M, and E proteins for trial B-21 and another 53 common ones, plus some new ones derived from the virus' main genetic variants for complementary trial C-21. Peptide selection was based on tremendous SARS-CoV-2 genetic variability for analysing them concerning vast human immunogenetic polymorphism for developing the first supramutational, Colombian SARS-protection (SM-COLSARSPROT), peptide mixture. Specific physicochemical rules were followed, i.e., aa predilection for polyproline type II left-handed (PPIIL) formation, replacing β-branched, aromatic aa, short-chain backbone H-bond-forming residues, π-π interactions (n→π* and π-CH), aa interaction with π systems, and molecular fragments able to interact with them, disrupting PPIIL propensity formation. All these modified structures had PPIIL formation propensity to enable target peptide interaction with human leukocyte antigen-DRβ1* (HLA-DRβ1*) molecules to mediate antigen presentation and induce an appropriate immune response. Such modified peptides were designed for human use; however, they induced high antibody titres against S, M, and E parental mutant peptides and neutralising antibodies when suitably modified and chemically synthesised for immunising 61 major histocompatibility complex class II (MHCII) DNA genotyped Aotus monkeys (matched with their corresponding HLA-DRβ1* molecules), predicted to cover 77.5% to 83.1% of the world's population. Such chemically synthesised peptide mixture represents an extremely pure, stable, reliable, and cheap vaccine for COVID-19 pandemic control, providing a new approach for a logical, rational, and soundly established methodology for other vaccine development.
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Affiliation(s)
- Manuel A. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Laura Pabón
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha P. Alba
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Adriana Bermudez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Díaz-Arevalo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Isabel Zapata
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - César Reyes
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carlos F. Suarez
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - William Agudelo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Carolina López
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jorge Aza-Conde
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Miguel Melo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luis Escamilla
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jairo Oviedo
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Fanny Guzmán
- Núcleo de Biotecnología, Pontificia U. Católica de Valparaíso, Valparaíso, Chile
| | - Yolanda Silva
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Martha Forero
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Lizdany Flórez-Álvarez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Armando Moreno-Vranich
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Jason Garry
- Grupos: Síntesis Química, Resonancia Magnética Nuclear y Cálculo Estructural, Biología Molecular e Inmunología e Inmuno-Química, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Catalina Avendaño
- Facultad de Ciencias Agropecualrias, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
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11
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Stanton SA, Du JJ, Lai F, Stanton G, Hawkins BA, Ong JA, Groundwater PW, Platts JA, Hibbs DE. Understanding Hygroscopicity of Theophylline via a Novel Cocrystal Polymorph: A Charge Density Study. J Phys Chem A 2021; 125:9736-9756. [PMID: 34731566 DOI: 10.1021/acs.jpca.0c09536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The charge density distribution in a novel cocrystal (1) complex of 1,3-dimethylxanthine (theophylline) and propanedioic acid (malonic acid) has been determined. The molecules crystallize in the triclinic, centrosymmetric space group P1̅, with four independent molecules (Z = 4) in the asymmetric unit (two molecules each of theophylline and malonic acid). Theophylline has a notably high hygroscopic nature, and numerous cocrystals have shown a significant improvement in stability to humidity. A charge density study of the novel polymorph has identified interesting theoretical results correlating the stability enhancement of theophylline via cocrystallization. Topological analysis of the electron density highlighted key differences (up to 17.8) in Laplacian (∇2ρ) between the experimental (EXP) and single-point (SP) models, mainly around intermolecular-bonded carbonyls. Further investigation via molecular electrostatic potential maps reaffirmed that the charge redistribution enhanced intramolecular hydrogen bonding, predominantly for N(2') and N(2) (61.2 and 61.8 kJ mol-1, respectively). An overall weaker lattice energy of the triclinic form (-126.1 kJ mol-1) compared to that of the monoclinic form (-133.8 kJ mol-1) suggests a lower energy threshold to overcome to initiate dissociation. Future work via physical testing of the novel cocrystal in both dissolution and solubility will further solidify the correlation between theoretical and experimental results.
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Affiliation(s)
- Stephen A Stanton
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathan J Du
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Felcia Lai
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gyte Stanton
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bryson A Hawkins
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jennifer A Ong
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul W Groundwater
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - James A Platts
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - David E Hibbs
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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12
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Wen W, Huang D, Bao J, Zhang JZH. Residue-specific binding mechanisms of PD-L1 to its monoclonal antibodies by computational alanine scanning. Phys Chem Chem Phys 2021; 23:15591-15600. [PMID: 34259259 DOI: 10.1039/d1cp01281a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Programmed cell death 1 receptor (PD-1) on the surface of T cells and its ligand 1 (PD-L1) are immune checkpoint proteins. Treating cancer patients with inhibitors blocking this checkpoint has significantly prolonged the survival rate of patients. In this study, we examined several monoclonal antibodies (mAbs) of PD-L1 and studied their detailed binding mechanism to PD-L1. An efficient computational alanine scanning method was used to perform quantitative analysis of hotspot residues that are important for PD-1/PD-L1 binding. A total of five PD-L1/mAb complexes were investigated and hotspots on both PD-L1 and mAbs were predicted. Our result shows that PD-L1M115 and PD-L1Y123 are two relatively important hotspots in all the five PD-L1/mAb binding complexes. It is also found that the important residues of mAbs binding to PD-L1M115 and PD-L1Y123 are similar to each other. The computational alanine scanning result is compared to the experimental measurements that are available for two of the mAbs (KN035 and atezolizumab). The calculated alanine scanning result is in good agreement with the experimental data with a correlation coefficient of 0.87 for PD-L1/KN035 and 0.6 for PD-L1/atezolizumab. Our computation found more hotspots on PD-L1 in the PD-L1/KN035 complex than those in the PD-L1/atezolizumab system, indicating stronger binding affinity in the former than the latter, which is in good agreement with the experimental finding. The present work provides important insights for the design of new mAbs targeting PD-L1.
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Affiliation(s)
- Wei Wen
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Dading Huang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jingxiao Bao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China. and Department of Chemistry, New York University, NY, NY 10003, USA and Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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13
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Li X, Sun W, Qin X, Xie Y, Liu N, Luo X, Wang Y, Chen X. An interesting possibility of forming special hole stepping stones with high-stacking aromatic rings in proteins: three-π five-electron and four-π seven-electron resonance bindings. RSC Adv 2021; 11:26672-26682. [PMID: 35479969 PMCID: PMC9037495 DOI: 10.1039/d1ra05341h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 11/30/2022] Open
Abstract
Long-range hole transfer of proteins plays an important role in many biological processes of living organisms. Therefore, it is highly useful to examine the possible hole stepping stones, which can facilitate hole transfer in proteins. However, the structures of stepping stones are diverse because of the complexity of the protein structures. In the present work, we proposed a series of special stepping stones, which are instantaneously formed by three and four packing aromatic side chains of amino acids to capture a hole, corresponding to three-π five-electron (π:π∴π↔π∴π:π) and four-π seven-electron (π:π∴π:π↔π:π:π∴π) resonance bindings with appropriate binding energies. The aromatic amino acids include histidine (His), phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp). The formations of these special stepping stones can effectively reduce the local ionization potential of the high π-stacking region to efficiently capture the migration hole. The quick formations and separations of them promote the efficient hole transfer in proteins. More interestingly, we revealed that a hole cannot delocalize over infinite aromatic rings along the high π-π packing structure at the same time and the micro-surroundings of proteins can modulate the formations of π:π∴π↔π∴π:π and π:π∴π:π↔π:π:π∴π bindings. These results may contribute a new avenue to better understand the potential hole transfer pathway in proteins.
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Affiliation(s)
- Xin Li
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Weichao Sun
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Yuxin Xie
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Nian Liu
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Xin Luo
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Yuanying Wang
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University Chongqing 401331 P.R. China
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University Chongqing 401331 P.R. China
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14
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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15
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Mohapatra SB, Manoj N. A conserved π-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140523. [PMID: 32853774 DOI: 10.1016/j.bbapap.2020.140523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Here, we characterize the role of a π-helix in the molecular mechanisms underlying thermoadaptation in the glycoside hydrolase family 4 (GH4). The interspersed π-helix present in a subgroup is evolutionarily related to a conserved α-helix in other orthologs by a single residue insertion/deletion event. The insertional residue, Phe407, in a hyperthermophilic α-glucuronidase, makes specific interactions across the inter-subunit interface. In order to establish the sequence-structure-stability implications of the π-helix, the wild-type and the deletion variant (Δ407) were characterized. The variant showed a significant lowering of melting temperature and optimum temperature for the highest activity. Crystal structures of the proteins show a transformation of the π-helix to a continuous α-helix in the variant, identical to that in orthologs lacking this insertion. Thermodynamic parameters were determined from stability curves representing the temperature dependence of unfolding free energy. Though the proteins display maximum stabilities at similar temperatures, a higher melting temperature in the wild-type is achieved by a combination of higher enthalpy and lower heat capacity of unfolding. Comparisons of the structural changes, and the activity and thermodynamic profiles allow us to infer that specific non-covalent interactions, and the existence of residual structure in the unfolded state, are crucial determinants of its thermostability. These features permit the enzyme to balance the preservation of structure at a higher temperature with the thermodynamic stability required for optimum catalysis.
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Affiliation(s)
- Samar Bhallabha Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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16
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Andersson CD, Mishra BK, Forsgren N, Ekström F, Linusson A. Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu. J Phys Chem B 2020; 124:6529-6539. [PMID: 32610016 PMCID: PMC7467712 DOI: 10.1021/acs.jpcb.0c03778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/26/2020] [Indexed: 11/28/2022]
Abstract
Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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Affiliation(s)
| | - Brijesh Kumar Mishra
- International
Institute of Information Technology, Bangalore, Karnataka 560003, India
| | - Nina Forsgren
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Fredrik Ekström
- CBRN
Defense and Security, Swedish Defense Research
Agency, SE-90621 Umeå, Sweden
| | - Anna Linusson
- Department
of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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17
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Al-Madhagi LH, Callear SK, Schroeder SLM. Hydrophilic and hydrophobic interactions in concentrated aqueous imidazole solutions: a neutron diffraction and total X-ray scattering study. Phys Chem Chem Phys 2020; 22:5105-5113. [DOI: 10.1039/c9cp05993h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study of 5 M aqueous imidazole solutions combining neutron and X-ray diffraction with EPSR simulations shows dominance of hydrogen-bonding between imidazole and water and negligible hydrogen-bonding between imidazole molecules.
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Affiliation(s)
- Laila H. Al-Madhagi
- School of Chemical and Process Engineering
- University of Leeds
- Leeds LS2 9JT
- UK
- Diamond Light Source Ltd
| | | | - Sven L. M. Schroeder
- School of Chemical and Process Engineering
- University of Leeds
- Leeds LS2 9JT
- UK
- Diamond Light Source Ltd
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18
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Claverie M, Cioci G, Guionnet M, Schörghuber J, Lichtenecker R, Moulis C, Remaud-Simeon M, Lippens G. Futile Encounter Engineering of the DSR-M Dextransucrase Modifies the Resulting Polymer Length. Biochemistry 2019; 58:2853-2859. [DOI: 10.1021/acs.biochem.9b00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Marion Claverie
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Gianluca Cioci
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Matthieu Guionnet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Claire Moulis
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | | | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
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19
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Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment. Molecules 2019; 24:molecules24010179. [PMID: 30621295 PMCID: PMC6337464 DOI: 10.3390/molecules24010179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/29/2018] [Accepted: 01/01/2019] [Indexed: 11/16/2022] Open
Abstract
Calculation of structural features of proteins, nucleic acids, and nucleic acid-protein complexes on the basis of their geometries and studying various interactions within these macromolecules, for which high-resolution structures are stored in Protein Data Bank (PDB), require parsing and extraction of suitable data stored in text files. To perform these operations on large scale in the face of the growing amount of macromolecular data in public repositories, we propose to perform them in the distributed environment of Azure Data Lake and scale the calculations on the Cloud. In this paper, we present dedicated data extractors for PDB files that can be used in various types of calculations performed over protein and nucleic acids structures in the Azure Data Lake. Results of our tests show that the Cloud storage space occupied by the macromolecular data can be successfully reduced by using compression of PDB files without significant loss of data processing efficiency. Moreover, our experiments show that the performed calculations can be significantly accelerated when using large sequential files for storing macromolecular data and by parallelizing the calculations and data extractions that precede them. Finally, the paper shows how all the calculations can be performed in a declarative way in U-SQL scripts for Data Lake Analytics.
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20
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Choudhury C, Narahari Sastry G. Pharmacophore Modelling and Screening: Concepts, Recent Developments and Applications in Rational Drug Design. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-05282-9_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Mason TO, Buell AK. The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:61-112. [PMID: 31713197 DOI: 10.1007/978-981-13-9791-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid β sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DTU, Lyngby, Denmark.
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22
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Dimitriou PS, Denesyuk AI, Nakayama T, Johnson MS, Denessiouk K. Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes. Protein Sci 2018; 28:344-364. [PMID: 30311984 DOI: 10.1002/pro.3527] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022]
Abstract
The alpha/beta-hydrolases (ABH) are among the largest structural families of proteins that are found in nature. Although they vary in their sequence and function, the ABH enzymes use a similar acid-base-nucleophile catalytic mechanism to catalyze reactions on different substrates. Because ABH enzymes are biocatalysts with a wide range of potential applications, protein engineering has taken advantage of their catalytic versatility to develop enzymes with industrial applications. This study is a comprehensive analysis of 40 ABH enzyme families focusing on two identified substructures: the nucleophile zone and the oxyanion zone, which co-ordinate the catalytic nucleophile and the residues of the oxyanion hole, and independently reported as critical for the enzymatic activity. We also frequently observed an aromatic cluster near the nucleophile and oxyanion zones, and opposite the ligand-binding site. The nucleophile zone, the oxyanion zone and the residue cluster enriched in aromatic side chains comprise a three-dimensional structural organization that shapes the active site of ABH enzymes and plays an important role in the enzymatic function by structurally stabilizing the catalytic nucleophile and the residues of the oxyanion hole. The structural data support the notion that the aromatic cluster can participate in co-ordination of the catalytic histidine loop, and properly place the catalytic histidine next to the catalytic nucleophile.
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Affiliation(s)
- Polytimi S Dimitriou
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander I Denesyuk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, 142290, Russia
| | - Toru Nakayama
- Tohoku University, Biomolecular Engineering, Sendai, Miyagi, 980-8579, Japan
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland.,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
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Uppula P. Exploration of Conformations, Analysis of Protein and Biological Significance of Histidine Dimers. ChemistrySelect 2018. [DOI: 10.1002/slct.201702559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Purushotham Uppula
- Center for molecular modelling; Indian Institute of Chemical Technology; Tarnaka Hyderabad-500 007 India
- Department of Chemistry; K L Education Foundation, Guntur; Andhra Pradesh India- 522502
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Andrić JM, Antonijević IS, Janjić GV, Zarić SD. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. J Mol Model 2018; 24:60. [PMID: 29464387 DOI: 10.1007/s00894-017-3570-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/14/2017] [Indexed: 11/30/2022]
Abstract
Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.
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Affiliation(s)
- Jelena M Andrić
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Ivana S Antonijević
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia. .,Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar.
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25
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Ribić VR, Stojanović SĐ, Zlatović MV. Anion–π interactions in active centers of superoxide dismutases. Int J Biol Macromol 2018; 106:559-568. [DOI: 10.1016/j.ijbiomac.2017.08.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023]
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26
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Khrustalev VV, Khrustaleva TA, Lelevich SV. Ethanol binding sites on proteins. J Mol Graph Model 2017; 78:187-194. [PMID: 29078103 DOI: 10.1016/j.jmgm.2017.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 01/19/2023]
Abstract
This study is on the analysis of ethanol binding sites on 3D structures of nonredundant proteins from the Protein Data Bank. The only one amino acid residue that is significantly overrepresented around ethanol molecules is Tyr. There are usually two or more Tyr residues in the same ethanol binding site, while residues of Thr, Asp and Gln are underrepresented around them. Residues of Ala and Pro are significantly underrepresented in ethanol binding surfaces. Several residues (Phe, Val, Pro, Ala, Arg, His, Ser, Asp) bind ethanol significantly more frequent if they are not included in beta strands. Residues of Ala, Ile and Arg preferably bind ethanol when they are included in an alpha helix. Ethanol molecules often make hydrogen bonds with oxygen and nitrogen atoms from the main chain of a protein. Because of this reason, the binding of ethanol may be associated with the decrease of the length of alpha helices and the disappearance of 3/10 helices. Obtained data should be useful for studies on new targets of the direct action of ethanol on enzymes, receptors, and transcription factors.
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Affiliation(s)
| | | | - Sergey Vladimirovich Lelevich
- Department of Clinical Laboratory Diagnostics, Allergology and Immunology, Grodno State Medical University, Gorkogo 80, Grodno, Belarus
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28
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Fernández ACR, Castellani NJ. Noncovalent Interactions between Dopamine and Regular and Defective Graphene. Chemphyschem 2017; 18:2065-2080. [DOI: 10.1002/cphc.201700252] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/10/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Ana C. Rossi Fernández
- IFISUR, Universidad Nacional del Sur, CONICET; Departamento de Física; Av. L. N. Alem 1253 B8000CPB Bahía Blanca Argentina
| | - Norberto J. Castellani
- IFISUR, Universidad Nacional del Sur, CONICET; Departamento de Física; Av. L. N. Alem 1253 B8000CPB Bahía Blanca Argentina
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29
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Reyes C, Moreno-Vranich A, Patarroyo ME. The role of pi-interactions and hydrogen bonds in fully protective synthetic malaria vaccine development. Biochem Biophys Res Commun 2017; 484:501-507. [DOI: 10.1016/j.bbrc.2017.01.077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
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30
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Shakourian-Fard M, Kamath G. The effect of defect types on the electronic and optical properties of graphene nanoflakes physisorbed by ionic liquids. Phys Chem Chem Phys 2017; 19:4383-4395. [PMID: 28119976 DOI: 10.1039/c6cp07455c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Defect engineering and non-covalent interaction strategies allow for dramatically tuning the optoelectronic properties of graphene. Using ab initio density functional theory (M06-2X/cc-pVDZ), we find that the nature of defects on the graphene nanoflakes (GNFs) and the size of defective GNF (DGNF) surfaces affect the binding energy (ΔEb) of ionic liquids (ILs) and the UV-Vis absorption spectra of DGNFIL complexes. Further, our results indicate that increasing the size of DGNFs affects the geometrical structure of the surfaces and increases the binding energy of ILs by about 10%. Analysis based on AIM and EDA shows that the interactions between ILs and DGNFs are non-covalent in nature (dispersion energy being dominant) and associated with charge transfer between the IL and nanoflakes. A comparison between the ΔEb values of ILs on DGNFs, GNFs, and h-BN nanoflakes (h-BNNF) shows that the presence of defects on the GNF surfaces increases the binding energy values as follows: DGNFIL > pristine GNFIL > h-BNNFIL. Our calculations indicate that increasing the size of DGNF surfaces leads to a decrease in the HOMO-LUMO energy gap (Eg) of the DGNF surfaces. Orbital energy and density of state calculations show that the Eg of DV(SW)-GNFs decreases upon IL adsorption and their Fermi energy level is shifted depending on the type of IL, thus enabling better conductivity. Reactivity descriptors generally indicate that the chemical potential (μ) and chemical hardness (η) of nanoflakes decrease upon IL adsorption, whereas the electrophilicity index (ω) increases. The UV-Vis absorption spectrum of DV-GNF and SW-GNF shows four bands in the visible spectrum which correspond to π → π* transitions with the absorption bands of SW-GNF appearing at higher wavelengths than those of DV-GNF. The most intense absorption bands in DV-GNF (λ = 348 nm) and SW-GNF (λ = 375 nm) are associated with electronic transitions HOMO-1 → LUMO+2 and HOMO → LUMO+1, respectively. In addition, these absorption bands undergo a red-shift by both increasing the size of the DV(SW)-GNF surfaces and IL adsorption. We also observe that the energy gaps and absorption spectra can be altered by varying the defect types and the type of IL adsorbate, where the defect types affect the spectral shapes of the bands and adsorbates at the first absorption peak, thus having potential application for light-emitting devices.
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Affiliation(s)
- Mehdi Shakourian-Fard
- Birjand University of Technology, Department of Chemical Engineering, Birjand, P.O. Box 97175/569, Iran.
| | - Ganesh Kamath
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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Sathiyashivan SD, Kumar CK, Shankar B, Sathiyendiran M, Masram DT. Perfect symmetrical cyclic aromatic trimer motif in tripodal molecule. RSC Adv 2017. [DOI: 10.1039/c7ra01682d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A family of substituted benzimidazolyl-based tripodal molecules with alkyl substituted spacers was synthesized, showing perfect symmetric cyclic aromatic trimer motifs which remained intact in the solid as well as solution state.
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32
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HajiEbrahimi A, Ghafouri H, Ranjbar M, Sakhteman A. Protein Ligand Interaction Fingerprints. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A most challenging part in docking-based virtual screening is the scoring functions implemented in various docking programs in order to evaluate different poses of the ligands inside the binding cavity of the receptor. Precise and trustable measurement of ligand-protein affinity for Structure-Based Virtual Screening (SB-VS) is therefore, an outstanding problem in docking studies. Empirical post-docking filters can be helpful as a way to provide various types of structure-activity information. Different types of interaction have been presented between the ligands and the receptor so far. Based on the diversity and importance of PLIF methods, this chapter will focus on the comparison of different protocols. The advantages and disadvantages of all methods will be discussed explicitly in this chapter as well as future sights for further progress in this field. Different classifications approaches for the protein-ligand interaction fingerprints were also discussed in this chapter.
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N-H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins. Biochemistry 2016; 55:3774-83. [PMID: 27305350 DOI: 10.1021/acs.biochem.6b00253] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The amino acid histidine can play a significant role in the structure and function of proteins. Its various functions include enzyme catalysis, metal binding activity, and involvement in cation-π, π-π, salt-bridge, and other types of noncovalent interactions. Although histidine's imidazole nitrogens (Nδ and Nε) are known to participate in hydrogen bond (HB) interactions as an acceptor or a donor, a systematic study of N-H···N HBs with the Nδ/Nε atom as the acceptor has not been conducted. In this study, we have examined two data sets of ultra-high-resolution (data set I) and very high-resolution (data set II) protein structures and identified 28 and 4017 examples of HBs of the N-H···Nδ/Nε type from both data sets involving histidine imidazole nitrogen as the acceptor. In nearly 70% of them, the main-chain N-H bond is the HB donor, and a majority of the examples are from the N-H group separated by two residues (Ni+2-Hi+2) from histidine. Quantum chemical calculations using model compounds were performed with imidazole and N-methylacetamide, and they assumed conformations from 19 examples from data set I with N-H···Nδ/Nε HBs. Basis set superposition error-corrected interaction energies varied from -5.0 to -6.78 kcal/mol. We also found that the imidazole nitrogen of 9% of histidine residues forming N-H···Nδ/Nε interactions in data set II participate in bifurcated HBs. Natural bond orbital analyses of model compounds indicate that the strength of each HB is mutually influenced by the other. Histidine residues involved in Ni+2-Hi+2···Nδi/Nεi HBs are frequently observed in a specific N-terminal capping position giving rise to a novel helix-capping motif. Along with their predominant occurrence in loop segments, we propose a new structural role for histidines in protein structures.
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35
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McDonald SK, Fleming KG. Aromatic Side Chain Water-to-Lipid Transfer Free Energies Show a Depth Dependence across the Membrane Normal. J Am Chem Soc 2016; 138:7946-50. [PMID: 27254476 DOI: 10.1021/jacs.6b03460] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitating and understanding the physical forces responsible for the interactions of biomolecules are fundamental to the biological sciences. This is especially challenging for membrane proteins because they are embedded within cellular bilayers that provide a unique medium in which hydrophobic sequences must fold. Knowledge of the energetics of protein-lipid interactions is thus vital to understand cellular processes involving membrane proteins. Here we used a host-guest mutational strategy to calculate the Gibbs free energy changes of water-to-lipid transfer for the aromatic side chains Trp, Tyr, and Phe as a function of depth in the membrane. This work reveals an energetic gradient in the transfer free energies for Trp and Tyr, where transfer was most favorable to the membrane interfacial region and comparatively less favorable into the bilayer center. The transfer energetics follows the concentration gradient of polar atoms across the bilayer normal that naturally occurs in biological membranes. Additional measurements revealed nearest-neighbor coupling in the data set are influenced by a network of aromatic side chains in the host protein. Taken together, these results show that aromatic side chains contribute significantly to membrane protein stability through either aromatic-aromatic interactions or placement at the membrane interface.
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Affiliation(s)
- Sarah K McDonald
- T.C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Karen G Fleming
- T.C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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36
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Pathan AAK, Panthi B, Khan Z, Koppula PR, Alanazi MS, Sachchidanand, Parine NR, Chourasia M. Lead identification for the K-Ras protein: virtual screening and combinatorial fragment-based approaches. Onco Targets Ther 2016; 9:2575-84. [PMID: 27217775 PMCID: PMC4861002 DOI: 10.2147/ott.s99671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE Kirsten rat sarcoma (K-Ras) protein is a member of Ras family belonging to the small guanosine triphosphatases superfamily. The members of this family share a conserved structure and biochemical properties, acting as binary molecular switches. The guanosine triphosphate-bound active K-Ras interacts with a range of effectors, resulting in the stimulation of downstream signaling pathways regulating cell proliferation, differentiation, and apoptosis. Efforts to target K-Ras have been unsuccessful until now, placing it among high-value molecules against which developing a therapy would have an enormous impact. K-Ras transduces signals when it binds to guanosine triphosphate by directly binding to downstream effector proteins, but in case of guanosine diphosphate-bound conformation, these interactions get disrupted. METHODS In the present study, we targeted the nucleotide-binding site in the "on" and "off" state conformations of the K-Ras protein to find out suitable lead compounds. A structure-based virtual screening approach has been used to screen compounds from different databases, followed by a combinatorial fragment-based approach to design the apposite lead for the K-Ras protein. RESULTS Interestingly, the designed compounds exhibit a binding preference for the "off" state over "on" state conformation of K-Ras protein. Moreover, the designed compounds' interactions are similar to guanosine diphosphate and, thus, could presumably act as a potential lead for K-Ras. The predicted drug-likeness properties of these compounds suggest that these compounds follow the Lipinski's rule of five and have tolerable absorption, distribution, metabolism, excretion and toxicity values. CONCLUSION Thus, through the current study, we propose targeting only "off" state conformations as a promising strategy for the design of reversible inhibitors to pharmacologically inhibit distinct conformations of K-Ras protein.
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Affiliation(s)
- Akbar Ali Khan Pathan
- Genome Research Chair (GRC), Department of Biochemistry, College of Science, King Saud University, Kingdom of Saudi Arabia; Integrated Gulf Biosystems, Riyadh, Kingdom of Saudi Arabia
| | - Bhavana Panthi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Zahid Khan
- Genome Research Chair (GRC), Department of Biochemistry, College of Science, King Saud University, Kingdom of Saudi Arabia
| | - Purushotham Reddy Koppula
- Department of Internal Medicine, School of Medicine, Columbia, MO, USA; Harry S. Truman Memorial Veterans Affairs Hospital, School of Medicine, Columbia, MO, USA; Department of Radiology, School of Medicine, Columbia, MO, USA
| | - Mohammed Saud Alanazi
- Genome Research Chair (GRC), Department of Biochemistry, College of Science, King Saud University, Kingdom of Saudi Arabia
| | - Sachchidanand
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Narasimha Reddy Parine
- Genome Research Chair (GRC), Department of Biochemistry, College of Science, King Saud University, Kingdom of Saudi Arabia
| | - Mukesh Chourasia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, India
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. Probing the Ca(2+)-assisted π-π interaction during Ca(2+)-dependent protein folding. SOFT MATTER 2016; 12:531-541. [PMID: 26489523 DOI: 10.1039/c5sm01796c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding is governed by a balance of non-covalent interactions, of which cation-π and π-π play important roles. Theoretical calculations revealed a strong cooperativity between cation-π involving alkali and alkaline earth metal ions and π-π interactions, but however, no experimental evidence was provided in this regard. Here, we characterized a Ca(2+)-binding self-processing module (SPM), which mediates a highly-specific Ca(2+)-dependent autocatalytic processing of iron-regulated protein FrpC secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis. The SPM undergoes a Ca(2+)-induced transition from an intrinsically unstructured conformation to the compact protein fold that is ultimately stabilized by the π-π interaction between two unique tryptophan residues arranged in the T-shaped orientation. Moreover, the pair of tryptophans is located in a close vicinity of a calcium-binding site, suggesting the involvement of a Ca(2+)-assisted π-π interaction in the stabilization of the tertiary structure of the SPM. This makes the SPM an excellent model for the investigation of the Ca(2+)-assisted π-π interaction during Ca(2+)-induced protein folding.
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Affiliation(s)
- Petra Matyska Liskova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 14200 Prague, Czech Republic.
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Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif. Structure 2015; 24:158-164. [PMID: 26712279 DOI: 10.1016/j.str.2015.10.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Abstract
The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.
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Sharma R, Sastry GN. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase. PLoS One 2015; 10:e0144294. [PMID: 26657745 PMCID: PMC4689552 DOI: 10.1371/journal.pone.0144294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Abstract
Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.
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Affiliation(s)
- Reetu Sharma
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India
| | - G. Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, 500007, India
- * E-mail:
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Redmile-Gordon MA, Evershed RP, Kuhl A, Armenise E, White RP, Hirsch PR, Goulding KW, Brookes PC. Engineering soil organic matter quality: Biodiesel Co-Product (BCP) stimulates exudation of nitrogenous microbial biopolymers. GEODERMA 2015; 259-260:205-212. [PMID: 26635420 PMCID: PMC4550076 DOI: 10.1016/j.geoderma.2015.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/01/2015] [Accepted: 06/07/2015] [Indexed: 05/31/2023]
Abstract
Biodiesel Co-Product (BCP) is a complex organic material formed during the transesterification of lipids. We investigated the effect of BCP on the extracellular microbial matrix or 'extracellular polymeric substance' (EPS) in soil which is suspected to be a highly influential fraction of soil organic matter (SOM). It was hypothesised that more N would be transferred to EPS in soil given BCP compared to soil given glycerol. An arable soil was amended with BCP produced from either 1) waste vegetable oils or 2) pure oilseed rape oil, and compared with soil amended with 99% pure glycerol; all were provided with 15N labelled KNO3. We compared transfer of microbially assimilated 15N into the extracellular amino acid pool, and measured concomitant production of exopolysaccharide. Following incubation, the 15N enrichment of total hydrolysable amino acids (THAAs) indicated that intracellular anabolic products had incorporated the labelled N primarily as glutamine and glutamate. A greater proportion of the amino acids in EPS were found to contain 15N than those in the THAA pool, indicating that the increase in EPS was comprised of bioproducts synthesised de novo. Moreover, BCP had increased the EPS production efficiency of the soil microbial community (μg EPS per unit ATP) up to approximately double that of glycerol, and caused transfer of 21% more 15N from soil solution into EPS-amino acids. Given the suspected value of EPS in agricultural soils, the use of BCP to stimulate exudation is an interesting tool to consider in the theme of delivering sustainable intensification.
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Affiliation(s)
- Marc A. Redmile-Gordon
- Dept. of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - Richard P. Evershed
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - Alison Kuhl
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - Elena Armenise
- School of Energy, Environment and Agrifood, Building 52a, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - Rodger P. White
- Dept. of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Penny R. Hirsch
- Dept. of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Keith W.T. Goulding
- Dept. of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Philip C. Brookes
- Dept. of Sustainable Soils and Grassland Systems, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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42
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Saha S, Sastry GN. Quantifying cooperativity in water clusters: an attempt towards obtaining a generalised equation. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1072648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Robillard DE, Mpangase PT, Hazelhurst S, Dehne F. SpeeDB: fast structural protein searches. Bioinformatics 2015; 31:3027-34. [PMID: 25979473 DOI: 10.1093/bioinformatics/btv274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/27/2015] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Interactions between amino acids are important determinants of the structure, stability and function of proteins. Several tools have been developed for the identification and analysis of such interactions in proteins based on the extensive studies carried out on high-resolution structures from Protein Data Bank (PDB). Although these tools allow users to identify and analyze interactions, analysis can only be performed on one structure at a time. This makes it difficult and time consuming to study the significance of these interactions on a large scale. RESULTS SpeeDB is a web-based tool for the identification of protein structures based on structural properties. SpeeDB queries are executed on all structures in the PDB at once, quickly enough for interactive use. SpeeDB includes standard queries based on published criteria for identifying various structures: disulphide bonds, catalytic triads and aromatic-aromatic, sulphur-aromatic, cation-π and ionic interactions. Users can also construct custom queries in the user interface without any programming. Results can be downloaded in a Comma Separated Value (CSV) format for further analysis with other tools. Case studies presented in this article demonstrate how SpeeDB can be used to answer various biological questions. Analysis of human proteases revealed that disulphide bonds are the predominant type of interaction and are located close to the active site, where they promote substrate specificity. When comparing the two homologous G protein-coupled receptors and the two protein kinase paralogs analyzed, the differences in the types of interactions responsible for stability accounts for the differences in specificity and functionality of the structures. AVAILABILITY AND IMPLEMENTATION SpeeDB is available at http://www.parallelcomputing.ca as a web service. CONTACT d@drobilla.net SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David E Robillard
- School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Phelelani T Mpangase
- School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Dehne
- School of Computer Science, Carleton University, Ottawa, Ontario, Canada, Sydney Brenner Institute for Molecular Bioscience and School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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Lovas S, He DZZ, Liu H, Tang J, Pecka JL, Hatfield MPD, Beisel KW. Glutamate transporter homolog-based model predicts that anion-π interaction is the mechanism for the voltage-dependent response of prestin. J Biol Chem 2015; 290:24326-39. [PMID: 26283790 DOI: 10.1074/jbc.m115.649962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 11/06/2022] Open
Abstract
Prestin is the motor protein of cochlear outer hair cells. Its unique capability to perform direct, rapid, and reciprocal electromechanical conversion depends on membrane potential and interaction with intracellular anions. How prestin senses the voltage change and interacts with anions are still unknown. Our three-dimensional model of prestin using molecular dynamics simulations predicts that prestin contains eight transmembrane-spanning segments and two helical re-entry loops and that tyrosyl residues are the structural specialization of the molecule for the unique function of prestin. Using site-directed mutagenesis and electrophysiological techniques, we confirmed that residues Tyr(367), Tyr(486), Tyr(501), and Tyr(508) contribute to anion binding, interacting with intracellular anions through novel anion-π interactions. Such weak interactions, sensitive to voltage and mechanical stimulation, confer prestin with a unique capability to perform electromechanical and mechanoelectric conversions with exquisite sensitivity. This novel mechanism is completely different from all known mechanisms seen in ion channels, transporters, and motor proteins.
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Affiliation(s)
- Sándor Lovas
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - David Z Z He
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Huizhan Liu
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Jie Tang
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Jason L Pecka
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Marcus P D Hatfield
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Kirk W Beisel
- From the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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Wilson KA, Wells RA, Abendong MN, Anderson CB, Kung RW, Wetmore SD. Landscape of π-π and sugar-π contacts in DNA-protein interactions. J Biomol Struct Dyn 2015; 34:184-200. [PMID: 25723403 DOI: 10.1080/07391102.2015.1013157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.
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Affiliation(s)
- Katie A Wilson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Rachael A Wells
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Minette N Abendong
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Colin B Anderson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Ryan W Kung
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Stacey D Wetmore
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
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Sharma B, Srivastava HK, Gayatri G, Sastry GN. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions. J Comput Chem 2015; 36:529-38. [DOI: 10.1002/jcc.23827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Bhaskar Sharma
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Hemant Kumar Srivastava
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Gaddamanugu Gayatri
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Garikapati Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
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Umadevi D, Narahari Sastry G. Graphane versus graphene: a computational investigation of the interaction of nucleobases, aminoacids, heterocycles, small molecules (CO2, H2O, NH3, CH4, H2), metal ions and onium ions. Phys Chem Chem Phys 2015; 17:30260-9. [DOI: 10.1039/c5cp05094d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compared the binding affinity of graphane and graphene with various molecules and ions.
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Affiliation(s)
- Deivasigamani Umadevi
- Centre for Molecular Modeling
- CSIR – Indian Institute of Chemical Technology
- Hyderabad - 500 607
- India
| | - G. Narahari Sastry
- Centre for Molecular Modeling
- CSIR – Indian Institute of Chemical Technology
- Hyderabad - 500 607
- India
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