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Rava G, Mahanta P. A Case Report of the Complete Union of an Impending Failure of Patellar Fracture Treated with Cannulated Cancellous Screws and Tension Band Wiring for Failed Modified Tension Band Wiring Technique. J Orthop Case Rep 2022; 12:5-8. [DOI: 10.13107/jocr.2022.v12.i04.2742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Introduction: Modified tension band wiring (MTBW) using two cannulated cancellous screws which also achieve a horizontal figure of eight patterns of tension band is established as a superior fixation to using Kirschner wires for type 34-C1 fracture of the patella. We are describing a case where this method was used for failed MTBW using two Kirschner wires where an impending failure in the early post-operative period proceeded to complete bony union without any implant failure or functional deficit following a period of conservative management. Case Presentation: We are describing a 67-year-old man with type 34-C1 fracture of patella treated by MTBW using Kirschner wires and a stainless steel (SS) wire, with fixation failure after around 6 weeks, which was revised by MTBW using two vertically placed cannulated partially threaded cancellous screws and SS wire as a tension band. In the early post-operative period, a routine X-ray of the operated part showed fracture fragment separation with a slight sack in the tension band wire without any signs of implant failure. To our surprise, the fracture proceeded to complete bony union while continuing gradually increased active knee range of motion exercises. Conclusion: This case report presents how an impending failure proceeded to complete fracture healing because of dynamic compression of the fracture provided by the tension band construct.
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Pandey S, Mahanta P, Berger BW, Acharya R. Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473. J Biol Chem 2021; 297:101014. [PMID: 34358563 PMCID: PMC8511899 DOI: 10.1016/j.jbc.2021.101014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/10/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/01/2022] Open
Abstract
Polysaccharide lyases (PLs) are a broad class of microbial enzymes that degrade anionic polysaccharides. Equally broad diversity in their polysaccharide substrates has attracted interest in biotechnological applications such as biomass conversion to value-added chemicals and microbial biofilm removal. Unlike other PLs, Smlt1473 present in the clinically relevant Stenotrophomonas maltophilia strain K279a demonstrates a wide range of pH-dependent substrate specificities toward multiple, diverse polysaccharides: hyaluronic acid (pH 5.0), poly-β-D-glucuronic (celluronic) acid (pH 7.0), poly-β-D-mannuronic acid, and poly-α-L-guluronate (pH 9.0). To decode the pH-driven multiple substrate specificities and selectivity in this single enzyme, we present the X-ray structures of Smlt1473 determined at multiple pH values in apo and mannuronate-bound states as well as the tetra-hyaluronate-docked structure. Our results indicate that structural flexibility in the binding site and N-terminal loop coupled with specific substrate stereochemistry facilitates distinct modes of entry for substrates having diverse charge densities and chemical structures. Our structural analyses of wild-type apo structures solved at different pH values (5.0–9.0) and pH-trapped (5.0 and 7.0) catalytically relevant wild-type mannuronate complexes (1) indicate that pH modulates the catalytic microenvironment for guiding structurally and chemically diverse polysaccharide substrates, (2) further establish that molecular-level fluctuation in the enzyme catalytic tunnel is preconfigured, and (3) suggest that pH modulates fluctuations resulting in optimal substrate binding and cleavage. Furthermore, our results provide key insight into how strategies to reengineer both flexible loop and regions distal to the active site could be developed to target new and diverse substrates in a wide range of applications.
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Affiliation(s)
- Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Pranjal Mahanta
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India
| | - Bryan W Berger
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States.
| | - Rudresh Acharya
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, 752050, Odisha, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India.
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Abstract
Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to their hidden nature, they are difficult to identify. Here, we show that small glycols find cryptic pockets on a diverse set of proteins. Initial crystallography experiments serendipitously revealed the ability of ethylene glycol, a small glycol, to identify a cryptic pocket on the W6A mutant of the RBSX protein (RBSX-W6A). Explicit-solvent molecular dynamics (MD) simulations of RBSX-W6A with the exposed state of the cryptic pocket (ethylene glycol removed) revealed closure of the pocket reiterating that the exposed state of cryptic pockets in general are unstable in the absence of ligands. Also, no change in the pocket was observed for simulations of RBSX-W6A with the occluded state of the cryptic pocket, suggesting that water molecules are not able to open the cryptic pocket. "Cryptic-pocket finding" potential of small glycols was then supported and generalized through additional crystallography experiments, explicit-cosolvent MD simulations, and protein data set construction and analysis. The cryptic pocket on RBSX-W6A was found again upon repeating the crystallography experiments with another small glycol, propylene glycol. Use of ethylene glycol as a probe molecule in cosolvent MD simulations led to the enhanced sampling of the exposed state of experimentally observed cryptic sites on a test set of two proteins (Niemann-Pick C2, Interleukin-2). Further, analyses of protein structures with validated cryptic sites showed that ethylene glycol molecules bind to sites on proteins (Bcl-xL, G-actin, myosin II, and glutamate receptor 2), which become apparent upon binding of biologically relevant ligands. Our study thus suggests potential application of the small glycols in experimental and computational fragment-based approaches to identify cryptic pockets in apparently undruggable and/or difficult targets, making these proteins amenable to drug-design strategies.
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Affiliation(s)
- Harsh Bansia
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
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Tripathy B, Mohanlal S, Mahanta P, Sharma N, Acharya R. Probing effect of packing motif on helical assembly. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Bansia H, Mahanta P, Ramakumar S. Certain small glycols as cryptic pocket finders in proteins. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s205327331709310x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Pandey S, MacDonald LC, Mahanta P, Berger BW, Acharya R. From structure to function: Smlt1473, a pH-dependent polysaccharide lyase. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317094104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mahanta P, Berger BW, Acharya R. Structure-based mechanistic insights into the biomineralization of CdS quantum dot. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317083486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Zayoud A, Mahanta P, Saha UK. Pure Oxy-Fuel Circulating Fluidized Bed Combustion by Controlling Adiabatic Flame Temperature Using Fuel Staging. CURR SCI INDIA 2017. [DOI: 10.18520/cs/v113/i08/1560-1567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mahanta P, Bhardwaj A, Kumar K, Reddy VS, Ramakumar S. Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (β/α)8-triosephosphate isomerase barrel enzyme. FEBS J 2015; 282:3543-55. [DOI: 10.1111/febs.13355] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/12/2015] [Accepted: 06/19/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Pranjal Mahanta
- Department of Physics; Indian Institute of Science; Bangalore India
| | - Amit Bhardwaj
- Plant Transformation Group; International Centre for Genetic Engineering and Biotechnology; New Delhi India
| | - Krishan Kumar
- Plant Transformation Group; International Centre for Genetic Engineering and Biotechnology; New Delhi India
| | - Vanga S. Reddy
- Plant Transformation Group; International Centre for Genetic Engineering and Biotechnology; New Delhi India
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Bhardwaj A, Mahanta P, Ramakumar S, Ghosh A, Leelavathi S, Reddy VS. Emerging role of N- and C-terminal interactions in stabilizing (β/α)8 fold with special emphasis on Family 10 xylanases. Comput Struct Biotechnol J 2012; 2:e201209014. [PMID: 24688655 PMCID: PMC3962208 DOI: 10.5936/csbj.201209014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [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: 08/17/2012] [Revised: 10/24/2012] [Accepted: 10/24/2012] [Indexed: 11/22/2022] Open
Abstract
Xylanases belong to an important class of industrial enzymes. Various xylanases have been purified and characterized from a plethora of organisms including bacteria, marine algae, plants, protozoans, insects, snails and crustaceans. Depending on the source, the enzymatic activity of xylanases varies considerably under various physico-chemical conditions such as temperature, pH, high salt and in the presence of proteases. Family 10 or glycosyl hydrolase 10 (GH10) xylanases are one of the well characterized and thoroughly studied classes of industrial enzymes. The TIM-barrel fold structure which is ubiquitous in nature is one of the characteristics of family 10 xylanases. Family 10 xylanases have been used as a “model system” due to their TIM-barrel fold to dissect and understand protein stability under various conditions. A better understanding of structure-stability-function relationships of family 10 xylanases allows one to apply these governing molecular rules to engineer other TIM-barrel fold proteins to improve their stability and retain function(s) under adverse conditions. In this review, we discuss the implications of N-and C-terminal interactions, observed in family 10 xylanases on protein stability under extreme conditions. The role of metal binding and aromatic clusters in protein stability is also discussed. Studying and understanding family 10 xylanase structure and function, can contribute to our protein engineering knowledge.
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Affiliation(s)
- Amit Bhardwaj
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149, Trieste, Italy
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bangalore, India
| | | | - Amit Ghosh
- National Institute of Cholera and Enteric diseases, Kolkata, India
| | - Sadhu Leelavathi
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Vanga Siva Reddy
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
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Ramakumar S, Mahanta P, Gupta S, Manoj BK. Comparison of surface fractal features of thermophilic and mesophilic proteins. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311098230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bhowmik DM, Dinda AK, Mahanta P, Agarwal SK. The evolution of the Banff classification schema for diagnosing renal allograft rejection and its implications for clinicians. Indian J Nephrol 2011; 20:2-8. [PMID: 20535263 PMCID: PMC2878403 DOI: 10.4103/0971-4065.62086] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Till the early 1990s there was no standardized international classification of renal allograft biopsies resulting in considerable heterogeneity in reporting among the various centers. A group of dedicated renal pathologists, nephrologists, and transplant surgeons developed a schema in Banff, Canada in 1991. Subsequently there have been updates at regular intervals. The following review presents the evolution of the Banff classification and its utility for clinicians.
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Affiliation(s)
- D M Bhowmik
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
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