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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bandyopadhyay AK, Ul Islam RN, Hazra N. Salt-Bridges in the Microenvironment of Stable Protein Structures. Bioinformation 2020; 16:900-909. [PMID: 34803266 PMCID: PMC8573455 DOI: 10.6026/97320630016900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 11/29/2022] Open
Abstract
Salt-bridges (sb) play an important role in the folding and stability of proteins. This is deduced from the evaluation of net energy in the microenvironments (ME, residues that are 4 Å away from positive and negative partners of salt-bridge and interact
with them). MEs act as a determinant of net-energy due to the intrinsic features in the sequence. The stability of extremophilic proteins is due to the presence of favorable residues at the ME without any unfavorable residues. We studied a dataset of four structures
from the protein data bank (PDB) and a homology model (1HM5) to gain insights on this issue. Data shows that the presence of isolated charges and polar residues in the core of extremophilic proteins helps in the formation of stable salt-bridges with reduced desolvation.
Thus, site-specific mutations with favorable residues at the ME will help to develop thermo stable proteins with strong salt bridges.
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Affiliation(s)
| | | | - Niladri Hazra
- Department of Zoology, University of Burdwan, West Bengal, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Islam RNU, Roy C, Gupta PSS, Banerjee S, Mitra D, Banerjee S, Bandyopadhyay AK. PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins. Bioinformation 2018; 14:190-193. [PMID: 30108414 PMCID: PMC6077827 DOI: 10.6026/97320630014190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 11/23/2022] Open
Abstract
Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB
that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical
procedure. It also classifies them in range specific and chain specific manners. It further computes percentage composition and
physicochemical properties along with residues propensities. It also prepares FASTA files for different segments (helix, strand and
coil) in the exact order that they follow in the sequence. Representative analyses on orthologous (homologous across species) proteins
demonstrate wide segmental variations of physicochemical properties. Such variations provide insights to relate the adaptation of
these proteins in a given functional constraint under diverse environmental conditions. Thus, the program finds applications in the
structural and evolutionary analysis of proteins.
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Affiliation(s)
| | - Chittran Roy
- Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
| | | | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
| | - Debanjan Mitra
- Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
| | - Sahini Banerjee
- Department of Biotechnology, Institute of Genetic Engineering, West Bengal, 700128, India
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Gupta PSS, Banerjee S, Islam RNU, Sur VP, Bandyopadhyay AK. Substitutional Analysis of Orthologous Protein Families Using BLOCKS. Bioinformation 2017; 13:1-7. [PMID: 28479743 PMCID: PMC5405086 DOI: 10.6026/97320630013001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 12/26/2016] [Accepted: 12/27/2016] [Indexed: 11/29/2022] Open
Abstract
Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and
biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be
understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Our
procedure APBEST uses BLOCK-FASTA file to extract BLOCK specific evolutionary parameters such as dominantly used hetero-pair
(D), usage of hetero-pairs (E), non-conservative to conservative substitution ratio (R), maximally-diverse residue (MDR), residue (RD)
and class (CD) specific diversity. All these parameters show BLOCK specific variation. Conservative nature of D points towards
restoration of function of BLOCK. While E sets the upper-limit of usage of hereto-pairs, strong correlation of R with divergence-rate
indicates that the later is directly dependent on non-conservative substitutions. The observation that MDR, measure of positional
diversity, occupy very limited positions in BLOCK indicates accommodation of diversity is positionally restricted. Overall, the study
extract observed hetero-pair related quantitative and multi-parametric details of BLOCK, which finds application in evolutionary
biology.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Vishma Pratap Sur
- Indian Institute of Chemical Biology, Animal House (IICB), Kolkata, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Banerjee S, Gupta PSS, Nayek A, Das S, Sur VP, Seth P, Islam RNU, Bandyopadhyay AK. PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2. Bioinformation 2015; 11:366-8. [PMID: 26339154 PMCID: PMC4546997 DOI: 10.6026/97320630011366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/23/2022] Open
Abstract
Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of
sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO
and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution
(PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides
users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of
Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized
outputs in excel format along with detailed methodology. The program package contains documentation describing application of
methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics.
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Affiliation(s)
| | | | | | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Nayek A, Gupta PSS, Banerjee S, Sur VP, Seth P, Das S, Islam RNU, Bandyopadhyay AK. ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2. Bioinformation 2015; 11:413-5. [PMID: 26420923 PMCID: PMC4574125 DOI: 10.6026/97320630011413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/17/2015] [Indexed: 12/02/2022] Open
Abstract
Component (bridge: ΔΔGbrd, background: ΔΔGprot, desolvation: ΔΔGdsolv) and net (ΔΔGnet) energy-terms of salt-bridge-structure
(SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS)
method. While the procedure reports gross energy terms (Kcal Mol-1), report on bond-multiplicity corrected normalized energyterms
(Kcal Mol-1 Bond-1) along with their accessibility (ASA) in monomer, isolated-SBS (ISBS) and networked-SBS (NSBS) format
would be very useful for statistical comparison among SBSs and understanding their location in protein structure. In this end,
ADSBET2 potentially incorporates these features along with additional model for side-chain. Gross and normalized energy-terms
are redirected in monomer, ISBS and NSBS format along with their ASA informations. It works on any number of SBSs for any
number of structure files present in a database. Taken together, ADSBET2 has been suitable for statistical analyses of SBSs
energetics and finds applications in protein engineering and structural bioinformatics.
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Affiliation(s)
| | | | | | - Vishma Pratap Sur
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Pratyay Seth
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Sunit Das
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal Kumar Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Gupta PSS, Mondal S, Mondal B, Islam RNU, Banerjee S, Bandyopadhyay AK. SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files. Bioinformation 2014; 10:164-6. [PMID: 24748757 PMCID: PMC3974244 DOI: 10.6026/97320630010164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 11/30/2022] Open
Abstract
Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In
hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein
structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges.
While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid
topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain
specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary
combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our
knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION
which can perform all the above mentioned computations for any number of protein with any number of chain at any given
distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses
potential for applications in the field of structural and comparative bioinformatics studies.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Sudipta Mondal
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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Gupta PSS, Banerjee S, Islam RNU, Mondal S, Mondal B, Bandyopadhyay AK. PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences. Bioinformation 2014; 10:105-7. [PMID: 24616564 PMCID: PMC3937585 DOI: 10.6026/97320630010105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/26/2014] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run. With a view to overcome above limitations, we have developed a standalone procedure i.e. PHYSICO, which performs various stages of computation in a single run based on the type of input provided either in RAW-FASTA or BLOCK-FASTA format and makes excel output for: a) Composition, Class composition, Mean molecular weight, Isoelectic point, Aliphatic index and GRAVY, b) column based compositions, variability and difference matrix, c) 25 kinds of window dependent sequence properties. The program is fast, efficient, error free and user friendly. Calculation of mean and standard deviation of homologous sequences sets, for comparison purpose when relevant, is another attribute of the program; a property seldom seen in existing GPL softwares. AVAILABILITY PHYSICO is freely available for non-commercial/academic user in formal request to the corresponding author akbanerjee@biotech.buruniv.ac.in.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Shyamashree Banerjee
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Rifat Nawaz Ul Islam
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Sudipta Mondal
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Buddhadev Mondal
- Department of Zoology, Burdwan Raj College, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
| | - Amal K Bandyopadhyay
- Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India
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