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Chompunud Na Ayudhya C, Graidist P, Tipmanee V. Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect. Sci Rep 2024; 14:12531. [PMID: 38822100 PMCID: PMC11143223 DOI: 10.1038/s41598-024-63505-x] [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: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.
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Affiliation(s)
- Chompunud Chompunud Na Ayudhya
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
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2
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Yamamoto K, Nagatoishi S, Matsunaga R, Nakakido M, Kuroda D, Tsumoto K. Conformational features and interaction mechanisms of V H H antibodies with β-hairpin CDR3: A case of Nb8-HigB2 interaction. Protein Sci 2023; 32:e4827. [PMID: 37916305 PMCID: PMC10661080 DOI: 10.1002/pro.4827] [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: 06/15/2023] [Revised: 10/07/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
The β-hairpin conformation is regarded as an important basic motif to form and regulate protein-protein interactions. Single-domain VH H antibodies are potential therapeutic and diagnostic tools, and the third complementarity-determining regions of the heavy chains (CDR3s) of these antibodies are critical for antigen recognition. Although the sequences and conformations of the CDR3s are diverse, CDR3s sometimes adopt β-hairpin conformations. However, characteristic features and interaction mechanisms of β-hairpin CDR3s remain to be fully elucidated. In this study, we investigated the molecular recognition of the anti-HigB2 VH H antibody Nb8, which has a CDR3 that forms a β-hairpin conformation. The interaction was analyzed by evaluation of alanine-scanning mutants, molecular dynamics simulations, and hydrogen/deuterium exchange mass spectrometry. These experiments demonstrated that positions 93 and 94 (Chothia numbering) in framework region 3, which is right outside CDR3 by definition, play pivotal roles in maintaining structural stability and binding properties of Nb8. These findings will facilitate the design and optimization of single-domain antibodies.
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Affiliation(s)
- Koichi Yamamoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
| | - Ryo Matsunaga
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Kuroda
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- Research Center for Drug and Vaccine DevelopmentNational Institute of Infectious DiseasesTokyoJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
- Medical Device Development and Regulation Research Center, School of EngineeringThe University of TokyoTokyoJapan
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Santos J, Castro T, Venâncio A, Silva C. Degradation of ochratoxins A and B by lipases: A kinetic study unraveled by molecular modeling. Heliyon 2023; 9:e19921. [PMID: 37809625 PMCID: PMC10559330 DOI: 10.1016/j.heliyon.2023.e19921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
Mycotoxins are toxic substances produced by fungi and, frequently, different mycotoxins cooccur in food commodities. Ochratoxin A (OTA) and Ochratoxin B (OTB) may co-occur in a variety of foods, like red wines and wheat, presenting a significant risk of population exposure. In this study, we investigated the potential of five lipases (Candida rugosa Lipase, Candida antarctica B Lipase, Thermomyces lanuginosus Lipase, Amano Lipase A from Aspergillus niger (ANL) and Porcine Pancreas Lipase (PPL)) to hydrolyze OTA and OTB into non-hazardous products. Only ANL and PPL degraded both substrates, however, with varying degrees of efficiency. PPL completely degraded OTB (9 h), but only 43% of OTA (25 h). Molecular simulations indicated a high binding energy of OTA to PPL, that can be explained by the impact of the chlorine group, impairing hydrolysis. ANL was able to completely degrade both mycotoxins, OTA in 3 h and OTB in 10 h. The ANL enzyme showed also high specificity to OTA, however, the activity of this enzyme is not affected by chlorine and hydrolyzes OTA faster than OTB. These two enzymes were found to be able to detoxify co-occurring ochratoxins A and B, making isolated enzymes an alternative to the direct use of microorganisms for mycotoxin mitigation in food.
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Affiliation(s)
- Joana Santos
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Tarsila Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Armando Venâncio
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, 4800-058, Guimarães, Portugal
| | - Carla Silva
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, 4710-057 Braga, 4800-058, Guimarães, Portugal
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4
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Rogowska A, Pryshchepa O, Som NN, Śpiewak P, Gołębiowski A, Rafińska K, Dobrucka R, Kurzydłowski K, Buszewski B, Pomastowski P. Study On The Zinc Ions Binding To Human Lactoferrin. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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5
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Investigations on the role of cation-π interactions in active centers of superoxide dismutase. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2022. [DOI: 10.2298/jsc220109013s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this study, we have analysed the influence of cation-? interactions on
stability and properties of superoxide dismutase (SOD) active centres. The
number of interactions formed by arginine is higher than lysine in the
cationic group, while histidine is comparatively higher in the ? group. The
energy contribution resulting from most frequent cation-? interactions was
in the lower range of strong hydrogen bonds. The cation-? interactions
involving transition metal ions as cation have energy more negative than
-418.4 kJ mol-1. Stabilization centres for these proteins showed that all
residues involved in cation-? interactions were important in locating one or
more of such centres. The majority of the residues involved in cation-p
interactions were evolutionarily conserved and might have a significant
contribution towards the stability of SOD proteins. The results presented in
this work can be very useful for understanding the contribution of cation-?
interactions to the stability of SOD active canters.
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Goswami S, Tripuramallu BK, Ganguly S. Structural perception into the supramolecular self-assembly directed by C H•••π and π•••π interactions of 5,15-di(4′-carboxyphenyl)-10,20-di(pyrenyl) zinc porphyrin linker. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Pandey B, Grover S, Goyal S, Jamal S, Singh A, Kaur J, Grover A. Novel missense mutations in gidB gene associated with streptomycin resistance in Mycobacterium tuberculosis: insights from molecular dynamics. J Biomol Struct Dyn 2018; 37:20-35. [DOI: 10.1080/07391102.2017.1417913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bharati Pandey
- Department of Biotechnology, Panjab University , Chandigarh 160014, India
| | - Sonam Grover
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi , New Delhi 110016, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University , Tonk 304022, Rajasthan, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University , Tonk 304022, Rajasthan, India
| | - Aditi Singh
- Department of Biotechnology, TERI University , Vasant Kunj, New Delhi 110070, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University , Chandigarh 160014, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University , New Delhi 110067, India
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8
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Rana S, Sahoo AR, Majhi BK. Structural complexes of the agonist, inverse agonist and antagonist bound C5a receptor: insights into pharmacology and signaling. MOLECULAR BIOSYSTEMS 2017; 12:1586-99. [PMID: 26978009 DOI: 10.1039/c6mb00031b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The C5a receptor (C5aR) is a pharmacologically important G-protein coupled receptor (GPCR) that interacts with (h)C5a, by recruiting both the "orthosteric" sites (site1 at the N-terminus and site2 at the ECS, extra cellular surface) on C5aR in a two site-binding model. However, the complex pharmacological landscape and the distinguishing chemistry operating either at the "orthosteric" site1 or at the functionally important "orthosteric" site2 of C5aR are still not clear, which greatly limits the understanding of C5aR pharmacology. One of the major bottlenecks is the lack of an experimental structure or a refined model structure of C5aR with appropriately defined active sites. The study attempts to understand the pharmacology at the "orthosteric" site2 of C5aR rationally by generating a highly refined full-blown model structure of C5aR through advanced molecular modeling techniques, and further subjecting it to automated docking and molecular dynamics (MD) studies in the POPC bilayer. The first series of structural complexes of C5aR respectively bound to a linear native peptide agonist ((h)C5a-CT), a small molecule inverse agonist (NDT) and a cyclic peptide antagonist (PMX53) are reported, apparently establishing the unique pharmacological landscape of the "orthosteric" site2, which also illustrates an energetically distinct but coherent competitive chemistry ("cation-π" vs. "π-π" interactions) involved in distinguishing the established ligands known for targeting the "orthosteric" site2 of C5aR. Over a total of 1 μs molecular dynamics (MD) simulation in the POPC bilayer, it is evidenced that while the agonist prefers a "cation-π" interaction, the inverse agonist prefers a "cogwheel/L-shaped" interaction in contrast to the "edge-to-face/T-shaped" type π-π interactions demonstrated by the antagonist by engaging the F275(7.28) of the C5aR. In the absence of a NMR or crystallographically guided model structure of C5aR, the computational model complexes not only provide valuable insights for understanding the C5aR pharmacology, but also emerge as a promising platform for the design and discovery of future potential drug candidates targeting the (h)C5a-C5aR signaling axes.
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Affiliation(s)
- Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
| | - Amita Rani Sahoo
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
| | - Bharat Kumar Majhi
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 751007, India.
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9
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Luo L, Wang XC, Ngo HH, Guo W. Thermodynamic entropy of organic oxidation in the water environment: experimental evaluation compared to semi-empirical calculation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:21350-21359. [PMID: 27502459 DOI: 10.1007/s11356-016-7324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Residual organic matters in the secondary effluent are usually less biodegradable in terms of the total organic carbon content, and when discharged into a receiving water body, their further decomposition most likely mainly occurs due to chemical oxidation. Using this scenario, a semi-empirical method was previously developed to calculate the thermodynamic entropy of organic oxidation to quantitatively evaluate the impact of organic discharge on the water environment. In this study, the relationship between the entropy increase (ΔSC) and excess organic mass (ΔTOC) was experimentally verified via combustion heat measurement using typical organic chemicals and mixtures. For individual organic chemicals, a linear relationship was detected between ΔSC and ΔTOC with the same proportionality coefficient, 54.0 kJ/g, determined in the previous semi-empirical relationship. For the organic mixtures, a linear relationship was also identified; however, the proportionality coefficient was 69.2 kJ/g, indicating an approximately 28 % increase in the oxidation heat required to decompose the same organic mass. This increase in energy can likely be attributed to the synergistic effects of hydrogen bonding, hydrophobic interactions, π-π interactions, and van der Waals interactions between functional groups of different organic compounds. Intermolecular interactions may result in 17-32 % more dissociation energy for organic mixtures compared to the organic components' chemical structures. Because organics discharged into a water body are always a mixture of organic compounds, the proportionality coefficient obtained using organic mixtures should be adopted to modify the previously proposed semi-empirical equation.
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Affiliation(s)
- Li Luo
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Xiaochang C Wang
- International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Key Lab of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology, Broadway, Sydney, NSW, 2007, Australia
| | - Wenshan Guo
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology, Broadway, Sydney, NSW, 2007, Australia
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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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Mucić ID, Nikolić MR, Stojanović SĐ. Contribution of cation-π interactions to the stability of Sm/LSm oligomeric assemblies. PROTOPLASMA 2015; 252:947-958. [PMID: 25408427 DOI: 10.1007/s00709-014-0727-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/30/2014] [Indexed: 06/04/2023]
Abstract
In this work, we have analyzed the influence of cation-π interactions to the stability of Sm/LSm assemblies and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while histidine is comparatively higher than phenylalanine and tyrosine in the π group. Arg-Tyr interactions are predominant among the various pairs analyzed. The furcation level of multiple cation-π interactions is much higher than that of single cation-π interactions in Sm/LSm interfaces. We have found hot spot residues forming cation-π interactions, and hot spot composition is similar for all aromatic residues. The Arg-Phe pair has the strongest interaction energy of -8.81 kcal mol(-1) among all the possible pairs of amino acids. The extent of burial of the residue side-chain correlates with the ΔΔG of binding for residues in the core and also for hot spot residues cation-π bonded across the interface. Secondary structure of the cation-π residues shows that Arg and Lys preferred to be in strand. Among the π residues, His prefers to be in helix, Phe prefers to be in turn, and Tyr prefers to be in strand. Stabilization centers for these proteins showed that all the five residues found in cation-π interactions are important in locating one or more of such centers. More than 50 % of the cation-π interacting residues are highly conserved. It is likely that the cation-π interactions contribute significantly to the overall stability of Sm/LSm proteins.
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Affiliation(s)
- Ivana D Mucić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
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12
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Wang F, Wan H, Hu JP, Chang S. Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C. MOLECULAR BIOSYSTEMS 2015; 11:223-31. [DOI: 10.1039/c4mb00383g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.
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Affiliation(s)
- Feng Wang
- School of Information Science & Engineering
- Changzhou University
- Changzhou
- China
| | - Hua Wan
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
| | - Jian-ping Hu
- Faculty of Biotechnology Industry
- Chengdu University
- Chengdu
- China
| | - Shan Chang
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
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13
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Frizzo CP, Tier AZ, Gindri IM, Meyer AR, Black G, Belladona AL, Martins MAP. Thermodynamic, energetic, and topological properties of crystal packing of pyrazolo[1,5-a]pyrimidines governed by weak electrostatic intermolecular interactions. CrystEngComm 2015. [DOI: 10.1039/c5ce00613a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The relationship between energetic and topological properties of crystals with weak electrostatic intermolecular interactions and thermodynamic data are presented.
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Affiliation(s)
- Clarissa P. Frizzo
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
| | - Aniele Z. Tier
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
| | - Izabelle M. Gindri
- Department of Bioengineering
- University of Texas at Dallas
- Richardson, USA
| | - Alexandre R. Meyer
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
| | - Gabrielle Black
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
| | - Andrei L. Belladona
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
| | - Marcos A. P. Martins
- NUQUIMHE
- Department of Chemistry
- Federal University of Santa Maria
- Santa Maria, Brazil
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14
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Zlatović MV, Borozan SZ, Nikolić MR, Stojanović SĐ. Anion–π interactions in protein–porphyrin complexes. RSC Adv 2015. [DOI: 10.1039/c5ra03373j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, we have analyzed the influence of anion–π interactions on the stability of high resolution protein–porphyrin complex crystal structures.
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Affiliation(s)
| | - Sunčica Z. Borozan
- Department of Chemistry
- Faculty of Veterinary Medicine
- University of Belgrade
- Belgrade
- Serbia
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Breberina LM, Milčić MK, Nikolić MR, Stojanović SĐ. Contribution of anion-π interactions to the stability of Sm/LSm proteins. J Biol Inorg Chem 2014; 20:475-85. [PMID: 25502146 DOI: 10.1007/s00775-014-1227-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/29/2014] [Indexed: 12/29/2022]
Abstract
We have analyzed the influence of anion-π interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-π interactions than Asp. Phe has the highest occurrence in these interactions than the other two π residues. Among the anion-π residue pairs, Glu-Phe residue pair showed the maximum number of anion-π. We have found hot-spot residues forming anion-π interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-π interacting residues identified in the dataset were involved in the formation of multiple anion-π interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-π interaction energies are distance and orientation dependent. It was found that anion-π interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-π interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same π-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-π interaction to the stability of Sm/LSm proteins.
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16
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Borozan SZ, Stojanović SĐ. Halogen bonding in complexes of proteins and non-natural amino acids. Comput Biol Chem 2013; 47:231-9. [DOI: 10.1016/j.compbiolchem.2013.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 12/15/2022]
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17
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Borozan SZ, Dimitrijević BP, Stojanović SĐ. Cation−π interactions in high resolution protein−RNA complex crystal structures. Comput Biol Chem 2013; 47:105-12. [DOI: 10.1016/j.compbiolchem.2013.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/01/2013] [Accepted: 08/19/2013] [Indexed: 12/27/2022]
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