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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [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: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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2
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Alakbaree M, Abdulsalam AH, Ahmed HH, Ali FH, Al-Hili A, Omar MSS, Alonazi M, Jamalis J, Latif NA, Hamza MA, Amran SI. A computational study of structural analysis of Class I human glucose-6-phosphate dehydrogenase (G6PD) variants: Elaborating the correlation to chronic non-spherocytic hemolytic anemia (CNSHA). Comput Biol Chem 2023; 104:107873. [PMID: 37141793 DOI: 10.1016/j.compbiolchem.2023.107873] [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: 03/02/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect that affects more than 500 million people worldwide. Individuals affected with G6PD deficiency may occasionally suffer mild-to-severe chronic hemolytic anemia. Chronic non-spherocytic hemolytic anemia (CNSHA) is a potential result of the Class I G6PD variants. This comparative computational study attempted to correct the defect in variants structure by docking the AG1 molecule to selected Class I G6PD variants [G6PDNashville (Arg393His), G6PDAlhambra (Val394Leu), and G6PDDurham (Lys238Arg)] at the dimer interface and structural NADP+ binding site. It was followed by an analysis of the enzyme conformations before and after binding to the AG1 molecule using the molecular dynamics simulation (MDS) approach, while the severity of CNSHA was determined via root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen bonds, salt bridges, radius of gyration (Rg), solvent accessible surface area analysis (SASA), and principal component analysis (PCA). The results revealed that G6PDNashville (Arg393His) and G6PDDurham (Lys238Arg) had lost the direct contact with structural NADP+ and salt bridges at Glu419 - Arg427 and Glu206 - Lys407 were disrupted in all selected variants. Furthermore, the AG1 molecule re-stabilized the enzyme structure by restoring the missing interactions. Bioinformatics approaches were also used to conduct a detailed structural analysis of the G6PD enzyme at a molecular level to understand the implications of these variants toward enzyme function. Our findings suggest that despite the lack of treatment for G6PDD to date, AG1 remains a novel molecule that promotes activation in a variety of G6PD variants.
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Affiliation(s)
- Maysaa Alakbaree
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.
| | | | - Haron H Ahmed
- Ibn Sina University for Medical and Pharmaceutical Sciences, Faculty of Medicine, Baghdad, Iraq
| | - Farah Hasan Ali
- Department of Radiology and Ultrasound, Al-Farahidi University, Collage of Medical Technology, Baghdad, Iraq
| | - Ahmed Al-Hili
- Department of Anesthesia, Al-Farahidi University, Collage of Medical Technology, Baghdad, Iraq
| | | | - Mona Alonazi
- Department of Biochemistry, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Nurriza Ab Latif
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Muaawia Ahmed Hamza
- Faculty of Medicine, King Fahad Medical City, Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Syazwani Itri Amran
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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3
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Ferruz N, Schmidt S, Höcker B. ProteinTools: a toolkit to analyze protein structures. Nucleic Acids Res 2021; 49:W559-W566. [PMID: 34019657 PMCID: PMC8262690 DOI: 10.1093/nar/gkab375] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/11/2021] [Accepted: 04/26/2021] [Indexed: 01/06/2023] Open
Abstract
The experimental characterization and computational prediction of protein structures has become increasingly rapid and precise. However, the analysis of protein structures often requires researchers to use several software packages or web servers, which complicates matters. To provide long-established structural analyses in a modern, easy-to-use interface, we implemented ProteinTools, a web server toolkit for protein structure analysis. ProteinTools gathers four applications so far, namely the identification of hydrophobic clusters, hydrogen bond networks, salt bridges, and contact maps. In all cases, the input data is a PDB identifier or an uploaded structure, whereas the output is an interactive dynamic web interface. Thanks to the modular nature of ProteinTools, the addition of new applications will become an easy task. Given the current need to have these tools in a single, fast, and interpretable interface, we believe that ProteinTools will become an essential toolkit for the wider protein research community. The web server is available at https://proteintools.uni-bayreuth.de.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Steffen Schmidt
- Computational Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
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4
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Banerjee S, Gupta PSS, Islam RNU, Bandyopadhyay AK. Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus. Sci Rep 2021; 11:11553. [PMID: 34078944 PMCID: PMC8172842 DOI: 10.1038/s41598-021-90723-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/13/2021] [Indexed: 12/04/2022] Open
Abstract
Salt-bridges play a key role in the thermostability of proteins adapted in stress environments whose intrinsic basis remains to be understood. We find that the higher hydrophilicity of PfP than that of HuP is due to the charged but not the polar residues. The primary role of these residues is to enhance the salt-bridges and their ME. Unlike HuP, PfP has made many changes in its intrinsic property to strengthen the salt-bridge. First, the desolvation energy is reduced by directing the salt-bridge towards the surface. Second, it has made bridge-energy more favorable by recruiting energetically advantageous partners with high helix-propensity among the six possible salt-bridge pairs. Third, ME-residues that perform intricate interactions have increased their energy contribution by making major changes in their binary properties. The use of salt-bridge partners as ME-residues, and ME-residues' overlapping usage, predominant in helices, and energetically favorable substitution are some of the favorable features of PfP compared to HuP. These changes in PfP reduce the unfavorable, increase the favorable ME-energy. Thus, the per salt-bridge stability of PfP is greater than that of HuP. Further, unfavorable target ME-residues can be identified whose mutation can increase the stability of salt-bridge. The study applies to other similar systems.
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Affiliation(s)
- Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur , Orissa, India
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5
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Ul Islam RN, Mitra D, Sen Gupta PS, Banerjee S, Mondal B, Bandyopadhyay AK. AUTOMINv1.0: an automation for minimization of Protein Data Bank files and its usage. Bioinformation 2019; 14:525-529. [PMID: 31435151 PMCID: PMC6681769 DOI: 10.6026/97320630014525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022] Open
Abstract
Global minimal structure of protein/enzyme is energetically compromised that maintains an intricate balance between the rigidity and
the flexibility. Such a state makes it interactive to its ligand molecules. Although protein data bank files (PDB) may have achieved the
state, in many situations minimization has been crucial to overcome unwanted steric clashes, and other conformational strains. It is
more so, when orthologous PDB structures that are intended in a given study, show variations in resolution, R-factor, shell-water
contents, loop characteristics etc. Here, a fully automated procedure of minimization would be highly useful. AUTOMINv1.0 is such
an automation of minimization that runs on any number of structure files with any number of chains in them along with the inclusion
of selective/non-selective shell-waters interacting with polar and or non-polar atom-types of protein. Comparison of the mean binaryitems
of salt-bridges of minimized and un-minimized structures (chains > 100) of nucleoside diphosphate kinase from mimi virus
shows dramatic improvements in the earlier. Again, the mean steric clashes of 2AZ3.pdb are reduced upon minimization. Remarkably,
the observed steric clashes between shell-waters and atom-types of protein are seen to be removed upon minimization. Taken together,
AUTOMINv1.0 is an automation of minimization that finds applications in structural bioinformatics.
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Affiliation(s)
- Rifat Nawaz Ul Islam
- Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India
| | - Debanjan Mitra
- Department of Biotechnology, TheUniversity of Burdwan, East Burdwan, West Bengal, India
| | | | - Sahini Banerjee
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, East Burdwan,West Bengal, India
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Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Yasmeen S, Goswami A. Insights from the salt bridge analysis of malate dehydrogenase from H. salinarum and E.coli. Bioinformation 2019; 15:95-103. [PMID: 31435155 PMCID: PMC6677910 DOI: 10.6026/97320630015095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 11/23/2022] Open
Abstract
Halophilic proteins have greater abundance of acidic over basic residues in sequence. In structure, the surface is decorated by negative
charges, with lower content of Lysine. Using sequence BLOCKs and 3D model of malate dehydrogenase from halophilic archaea
(Halobacterium salinarum; hsMDH) and X-ray structure from mesophilic bacteria (E. coli; ecMDH), we show that not only acidic and basic
residues have higher mean relative abundance (MRA) and thus, impart higher polarity to the sequences, but also show their presence in
the surface of the structure of hsMDH relative to its mesophilic counterpart. These observations may indicate that both the acidic and the
basic residues have a concerted role in the stability of hsMDH. Analysis on salt bridges from hsMDH and ecMDH show that in the former,
salt bridges are highly intricate, newly engineered and global in nature. Although, these salt bridges are abundant in hsMDH, in the active
site the design remains unperturbed. In high salt where hydrophobic force is weak, these salt bridges seem to play a major role in the
haloadaptation of the tertiary structure of hsMDH. This is the first report of such an observation.
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Affiliation(s)
| | | | - Debanjan Mitra
- Department of Biotechnology,The University of Burdwan,Burdwan, West Bengal,India
| | - Sahini Banerjee
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
| | - Saba Yasmeen
- Department of Botany and Microbiology,Acharya Nagarjun University,Nagarjun Nagar,Andra Pradesh,India
| | - Arunava Goswami
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
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Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A. Stability of buried and networked salt-bridges (BNSB)in thermophilic proteins. Bioinformation 2019; 15:61-67. [PMID: 31360001 PMCID: PMC6651030 DOI: 10.6026/97320630015061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/02/2019] [Indexed: 11/23/2022] Open
Abstract
Thermophilic proteins function at high temperature, unlike mesophilic proteins. Thermo-stability of these proteins is due to the unique buried and networked salt-bridge (BNSB). However, it is known that the desolvation cost of BNSB is too high compared to other favorable energy terms. Nonetheless, it is known that stability is provided generally by hydrophobic isosteres without the need for BNSB. We show in this analysis that the BNSB is the optimal evolutionary design of salt-bridge to offset desolvation cost efficiently. Hence, thermophilic proteins with a high level of BNSB provide thermo-stability.
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Affiliation(s)
| | | | - Debanjan Mitra
- Department of Biotechnology, University of Burdwan, Burdwan, West Bengal,India
| | - Sahini Banerjee
- Department of Biological Sciences, ISI, Kolkata, West Bengal,India
| | - Arunava Goswami
- Department of Biological Sciences, ISI, Kolkata, West Bengal,India
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8
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Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A. Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens. Bioinformation 2019; 15:214-225. [PMID: 31354198 PMCID: PMC6637400 DOI: 10.6026/97320630015214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 01/19/2023] Open
Abstract
Hyper thermophilic archaea not only tolerate high temperature but also operate its biochemical machineries, normally under these conditions. However, the structural signatures in proteins that answer for the hyper thermo-stability relative to its mesophilic homologue remains poorly understood. We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally non-conservative (PNCS), conservative (PCS), unchanged (PU) and interchanged (PIC) type of substitutions. PNCS-sbfrs constitutes 28% and it is associated with the topology of pfPOP at high temperature. PCS helps to increase the salt-bridge population. It is also found that PU maintains similar salt-bridges at the active site and other binding sites while PIC abolishes mesophilic patterns.
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Affiliation(s)
| | | | - Debanjan Mitra
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Sahini Banerjee
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
| | - Arunava Goswami
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
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9
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Banerjee S, Mondal B, Islam RNU, Gupta PSS, Mitra D, Bandyopadhyay A. POWAINDv1.0: A Program for Protein-Water Interactions Determination. Bioinformation 2019; 14:530-539. [PMID: 31223212 PMCID: PMC6563665 DOI: 10.6026/97320630014530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 12/06/2018] [Indexed: 11/23/2022] Open
Abstract
Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the
rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar
groups of amino acid residues and intermolecular weak interactions between these groups and shell-waters may contribute to the overall
stability of the tertiary structure. However, the question as to what are the dynamics of interactions of shell-water with respect to weak
forces and atom-groups of protein (AGP), requires systematic investigations. In this end, we have developed a procedure POWAINDv1.0
that analyzes interactions of crystallographic shell-waters (CSH) in residues and AGP specific manner. The shell-water and AGP specific
bridge-interactions are also extracted. Further, the program analyzes favorable and unfavorable nature of each interaction based on the
actual and 75% of the sum of van der Waals (vdW) radii of interacting atoms. The EXCEL-outputs are useful in understanding the profile
for AGP-CSH interactions and contribution of each component in AGP. Taken together, the program provides intricate details on CSHprotein
interactions and finds application in the structural Bioinformatics
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Affiliation(s)
- Sahini Banerjee
- Department of Biological Sciences, ISI, Kolkata, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj Collage, East Burdwan, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India
| | - Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India
| | - Debanjan Mitra
- Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India
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Bandyopadhyay AK, Islam RNU, Mitra D, Banerjee S, Goswami A. Structural insights from water-ferredoxin interaction in mesophilic algae and halophilic archaea. Bioinformation 2019; 15:79-89. [PMID: 31435153 PMCID: PMC6677902 DOI: 10.6026/97320630015079] [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: 01/09/2019] [Revised: 02/11/2019] [Accepted: 02/11/2018] [Indexed: 11/23/2022] Open
Abstract
We analyzed the water-ferredoxin interaction in mesophilic (moderate temperature) algae (PDB ID: 1AWD) and halophilic (salt-tolerant) archaea (PDB ID: 1DOI) using POWAIND version 2.0 (a protein-water interactions calculation program). It is found that the shell water (SW) is 2.5 fold greater in halophilic ferredoxin than mesophilic ferredoxin. Water-ferredoxin interactions in the core and cavity are the signature of stability. The normalized frequency of such interactions is less in halophilic relative to mesophilic ferredoxin and the halophilic signature for stability by such interactions is negligible. However, the surface dominated with such interactions seems to be important for ferredoxin and oxido-reductase recognition.
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Affiliation(s)
- Amal Kumar Bandyopadhyay
- Department of Biotechnology,The University of Burdwan,Burdwan, West Bengal,India,Amal Kumar Bandyopadhyay:
| | | | - Debanjan Mitra
- Department of Biotechnology,The University of Burdwan,Burdwan, West Bengal,India
| | - Sahini Banerjee
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
| | - Arunava Goswami
- Department of Biological Sciences,ISI,Kolkata,West Bengal,India
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11
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Borrel A, Camproux AC, Xhaard H. Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank. ACS OMEGA 2017; 2:7359-7374. [PMID: 31457307 PMCID: PMC6645025 DOI: 10.1021/acsomega.7b00739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/11/2017] [Indexed: 06/10/2023]
Abstract
We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 Å), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.
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Affiliation(s)
- Alexandre Borrel
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Anne-Claude Camproux
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
| | - Henri Xhaard
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
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12
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Banerjee S, Sen Gupta PS, Bandyopadhyay AK. Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India. BMC Immunol 2017; 18:13. [PMID: 28264652 PMCID: PMC5339996 DOI: 10.1186/s12865-017-0197-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 02/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes Japanese Encephalitis (JE) and Acute Encephalitis Syndrome (AES) in humans. Genotype-I (as co-circulating cases with Genotype-III) was isolated in 2010 (JEV28, JEV21) and then in 2011 (JEV45) from Midnapur district, West Bengal (WB) for the first time from clinical patients who were previously been vaccinated with live attenuated SA14-14-2 strain. We apply bioinformatics and immunoinformatics on sequence and structure of E protein for analysis of crucial substitutions that might cause the genotypic transition, affecting protein-function and altering specificity of epitopes. RESULTS Although frequency of substitutions in E glycoprotein of JEV28, JEV21 and JEV45 isolates vary, its homologous patterns remain exactly similar as earlier Japan isolate (Ishikawa). Sequence and 3D model-structure based analyses of E protein show that only four of all substitutions are critical for genotype-I specific effect of which N103K is common among all isolates indicating its role in the transition of genotype-III to genotype-I. Predicted B-cell and T-cell epitopes are seen to harbor these critical substitutions that affect overall conformational stability of the protein. These epitopes were subjected to conservation analyses using a large set of the protein from Asian continent. CONCLUSIONS The study identifies crucial substitutions that contribute to the emergence of genotype-I. Predicted epitopes harboring these substitutions may alter specificity which might be the reason of reported failure of vaccine. Conservation analysis of these epitopes would be useful for design of genotype-I specific vaccine.
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Affiliation(s)
- Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal 713104 India
| | - Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal 713104 India
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13
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Sowmya G, Ranganathan S. Discrete structural features among interface residue-level classes. BMC Bioinformatics 2015; 16 Suppl 18:S8. [PMID: 26679043 PMCID: PMC4682381 DOI: 10.1186/1471-2105-16-s18-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of PPIs. Each PPI complex is specific, sensitive and selective to binding. Therefore, we have estimated the relative difference in percentage of polar residues between surface and the interface for each complex in a non-redundant heterodimer dataset of 278 complexes to understand the predominant forces driving binding. RESULTS Our analysis showed ~60% of protein complexes with surface polarity greater than interface polarity (designated as class A). However, a considerable number of complexes (~40%) have interface polarity greater than surface polarity, (designated as class B), with a significantly different p-value of 1.66E-45 from class A. Comprehensive analyses of protein complexes show that interface features such as interface area, interface polarity abundance, solvation free energy gain upon interface formation, binding energy and the percentage of interface charged residue abundance distinguish among class A and class B complexes, while electrostatic visualization maps also help differentiate interface classes among complexes. CONCLUSIONS Class A complexes are classical with abundant non-polar interactions at the interface; however class B complexes have abundant polar interactions at the interface, similar to protein surface characteristics. Five physicochemical interface features analyzed from the protein heterodimer dataset are discriminatory among the interface residue-level classes. These novel observations find application in developing residue-level models for protein-protein binding prediction, protein-protein docking studies and interface inhibitor design as drugs.
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14
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Sowmya G, Breen EJ, Ranganathan S. Linking structural features of protein complexes and biological function. Protein Sci 2015; 24:1486-94. [PMID: 26131659 DOI: 10.1002/pro.2736] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 11/11/2022]
Abstract
Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions.
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Affiliation(s)
- Gopichandran Sowmya
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edmond J Breen
- Australian Proteome Analysis Facility (APAF), Macquarie University, Sydney, New South Wales 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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Gupta PSS, Nayek A, Banerjee S, Seth P, Das S, Sur VP, Roy C, Bandyopadhyay AK. SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2. Bioinformation 2015; 11:39-42. [PMID: 25780279 PMCID: PMC4349938 DOI: 10.6026/97320630011039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 12/14/2014] [Indexed: 11/24/2022] Open
Abstract
Specific electrostatics (i.e. salt-bridge) includes both local and non-local interactions that contribute to the overall stability of
proteins. It has been shown that a salt-bridge could either be buried or exposed, networked or isolated, hydrogen-bonded or nonhydrogen
bonded, in secondary-structure or in coil, formed by single or multiple bonds. Further it could also participates either in
intra- or inter-dipole interactions with preference in orientation either for basic residue at N-terminal (orientation-I) or acidic
residue at N-terminal (orientation-II). In this context SBION2 is unique in that it reports above mentioned binary items in excel
format along with details on intra and inter-dipole interactions and orientations. These results are suitable for post run statistical
analyses involving large datasets. Reports are also made on protein-protein interactions, intervening residue distances and general
residue specific salt-bridge details. A ready to use compact supplementary table is also produced. The program runs in three
alternative modes. Each mode works on any number of structure files with any number of chains at any given atomic distance of
ion-pair. Thus SBION2 provides intricate details on salt-bridges and finds application in structural bioinformatics.
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Affiliation(s)
| | | | | | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
| | - Chittran Roy
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104
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Nayek A, Sen Gupta PS, Banerjee S, Mondal B, Bandyopadhyay AK. Salt-bridge energetics in halophilic proteins. PLoS One 2014; 9:e93862. [PMID: 24743799 PMCID: PMC3990605 DOI: 10.1371/journal.pone.0093862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/07/2014] [Indexed: 11/19/2022] Open
Abstract
Halophilic proteins have greater abundance of acidic over basic and very low bulky hydrophobic residues. Classical electrostatic stabilization was suggested as the key determinant for halophilic adaptation of protein. However, contribution of specific electrostatic interactions (i.e. salt-bridges) to overall stability of halophilic proteins is yet to be understood. To understand this, we use Adaptive-Poison-Boltzmann-Solver Methods along with our home-built automation to workout net as well as associated component energy terms such as desolvation energy, bridge energy and background energy for 275 salt-bridges from 20 extremely halophilic proteins. We then perform extensive statistical analysis on general and energetic attributes on these salt-bridges. On average, 8 salt-bridges per 150 residues protein were observed which is almost twice than earlier report. Overall contributions of salt-bridges are −3.0 kcal mol−1. Majority (78%) of salt-bridges in our dataset are stable and conserved in nature. Although, average contributions of component energy terms are equal, their individual details vary greatly from one another indicating their sensitivity to local micro-environment. Notably, 35% of salt-bridges in our database are buried and stable. Greater desolvation penalty of these buried salt-bridges are counteracted by stable network salt-bridges apart from favorable equal contributions of bridge and background terms. Recruitment of extensive network salt-bridges (46%) with a net contribution of −5.0 kcal mol−1 per salt-bridge, seems to be a halophilic design wherein favorable average contribution of background term (−10 kcal mol−1) exceeds than that of bridge term (−7 kcal mol−1). Interiors of proteins from halophiles are seen to possess relatively higher abundance of charge and polar side chains than that of mesophiles which seems to be satisfied by cooperative network salt-bridges. Overall, our theoretical analyses provide insight into halophilic signature in its specific electrostatic interactions which we hope would help in protein engineering and bioinformatics studies.
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Affiliation(s)
- Arnab Nayek
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | | | - Shyamashree Banerjee
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, The University of Burdwan, Burdwan, West Bengal, India
| | - Amal K. Bandyopadhyay
- The Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- * E-mail:
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