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Tooley AA, Law J, Lelli GJ, Sun G, Godfrey KJ, Tran AQ, Kim E, Solomon JM, Chen JJ, Khan AR, Wayman L, Olson JH, Lee MS, Harrison AR, Espinoza GM, Davitt BV, Tao J, Hodge DO, Barkmeier AJ. Predictors of Ophthalmology Resident Performance From Medical Student Application Materials. Journal of Surgical Education 2024; 81:151-160. [PMID: 38036387 DOI: 10.1016/j.jsurg.2023.10.003] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 12/02/2023]
Abstract
OBJECTIVE To determine whether elements in ophthalmology residency applications are predictors of future resident performance. DESIGN This multi-institutional, cross-sectional, observational study retrospectively reviewed the residency application materials of ophthalmology residents who graduated from residency from 2006 through 2018. Resident performance was scored by 2 faculty reviewers in 4 domains (clinical, surgical, academic, and global performance). Correlation between specific elements of the residency application and resident performance was assessed by Spearman correlation coefficients (univariate) and linear regression (multivariate) for continuous variables and logistic regression (multivariate) for categorical variables. SETTING Seven ophthalmology residency programs in the US. PARTICIPANTS Ophthalmology residents who graduated from their residency program. RESULTS High-performing residents were a diverse group, in terms of sex, ethnicity, visa status, and educational background. Residents with United States Medical Licensing Examination Step 1 scores higher than the national average for that year had significantly higher scores in all 4 performance domains than those who scored at or below the mean (all domains P < 0.05). Residents who had honors in at least 4 core clerkships and who were members of Alpha Omega Alpha Medical Honor Society also had higher scores in all 4 performance domains (all domains P ≤ 0.04). Step 1 score (ρ=0.26, P < 0.001) and the difference between Step 1 score and the national average for that year (ρ=0.19, P = 0.009) positively correlated with total resident performance scores. Residents who passed the American Board of Ophthalmology Written Qualifying Examination or Oral Examination on their first attempt had significantly higher Step 1/2 scores (P ≤ 0.005), Ophthalmology Knowledge Assessment Program scores (P = 0.001), and resident performance scores (P ≤ 0.004). CONCLUSIONS In this new landscape of increasing numbers of applicants to residency programs and changing of the Step 1 score to pass/fail, our findings may help guide selection committees as they holistically review applicants to select exceptional future residents in ophthalmology.
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Affiliation(s)
- Andrea A Tooley
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota.
| | - Janice Law
- Department of Ophthalmology, Vanderbilt University, Nashville, Tennessee
| | - Gary J Lelli
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Grace Sun
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Kyle J Godfrey
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Ann Q Tran
- Department of Ophthalmology, Weill Cornell Medical College, New York, New York
| | - Eleanore Kim
- Department of Ophthalmology, New York University, New York, New York
| | - Joel M Solomon
- Department of Ophthalmology, New York University, New York, New York
| | - John J Chen
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Amir R Khan
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - Laura Wayman
- Department of Ophthalmology, Vanderbilt University, Nashville, Tennessee
| | - Joshua H Olson
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota
| | - Michael S Lee
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota
| | - Andrew R Harrison
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota
| | | | - Bradley V Davitt
- Department of Ophthalmology, Saint Louis University, St. Louis, Missouri
| | - Jeremiah Tao
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, California
| | - David O Hodge
- Division of Clinical Trials and Biostatistics, Mayo Clinic, Jacksonville, Florida
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Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. bioRxiv 2023:2023.05.09.539914. [PMID: 37214973 PMCID: PMC10197589 DOI: 10.1101/2023.05.09.539914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam J. Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B. Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- current address: Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nicholas P. Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
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Hamid R, Gomes VC, Huda N, Khan AR, Chowdhury M, Azam I. Role of Ommaya Reservoir in Pediatric Hydrocephalus: Experience in Bangladesh Medical College Hospital from 2019-2021. Mymensingh Med J 2023; 32:510-519. [PMID: 37002765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
The goal of this study was to analyze the efficacy of the Ommaya reservoir within all the different types of hydrocephalus in pediatric patients. At the same time, it's safe for repeated aspirations or long-term retention of the reservoir in the body. This retrospective, cross-sectional study was performed from January 2019 to December 2021, 33 consecutive cases of reservoir implantation were taken into the study irrespective of the etiology of hydrocephalus in the Neurosurgery Department of Bangladesh Medical College Hospital, Dhaka, Bangladesh. These were mostly placed along with endoscopic third ventriculostomy and some were placed as an intermediary procedure to combat shunt complications in emaciated infants. Cerebrospinal fluid (CSF) aspiration was done in case of failed endoscopic third ventriculostomy and the frequency of aspiration depended upon the production of cerebrospinal fluid. Acetazolamide was routinely administered in each patient to reduce the frequency of aspiration. Most of the patients required ventriculo-peritoneal (VP) shunt while they had sufficient body weight and few required no surgery. The average age at presentation was 76.88 days. All the neonates and infants had less weight in terms of their age. 42.4% of babies needed aspiration 2 times per week. Among all cases, 9.1% developed reservoir complications. Complications were not related to the number and volume of aspiration or duration of the reservoir in the body. Two (2) patients died after one year of reservoir implantation due to unknown etiology. Out of the 31 survivors, 3 patients did not need any further aspiration and 19 patients needed a ventriculo-peritoneal shunt, but the reservoir was kept in situ for a future emergency. The rest of them is waiting for a definitive shunt procedure. Other findings include low socioeconomic group was more prone to low birth weight and they carried the burden of congenital hydrocephalus and meningomyelocele. Most affected babies had their prenatal period in arsenic-affected areas in Bangladesh. Overall folic acid supplementation was started after the formation of the neural tube irrespective of socioeconomic status. Ommaya reservoir placement along with endoscopic third ventriculostomy plays a vital role in delaying shunt in endoscopic third ventriculostomy failure. It is a 'time buying' procedure until the baby has sufficient weight for successful shunt surgery. It has been found very effective intermediary intervention for managing shunt infection and it also helps revive a channel in shunt obstruction.
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Affiliation(s)
- R Hamid
- Professor Rezina Hamid, Head of Department of Neurosurgery, Bangladesh Medical College Hospital, Dhaka, Bangladesh; E-mail:
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Strofaldi A, Khan AR, McManus JJ. Surface Exposed Free Cysteine Suppresses Crystallization of Human γD-Crystallin. J Mol Biol 2021; 433:167252. [PMID: 34537240 DOI: 10.1016/j.jmb.2021.167252] [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: 07/23/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022]
Abstract
Human γD-crystallin (HGD) has remarkable stability against condensation in the human lens, sometimes over a whole lifetime. The native protein has a surface exposed free cysteine that forms dimers (Benedek, 1997; Ramkumar et al., 1864)1,2 without specific biological function and leads to further protein association and/or aggregation, which creates a paradox for understanding its stability. Previous work has demonstrated that chemical modification of the protein at the free cysteine (C110), increases the temperature at which liquid-liquid phase separation occurs (LLPS), lowers protein solubility and suggests an important role for this amino acid in maintaining its long-term resistance to condensation. Here we demonstrate that mutation of the cysteine does not alter the structure or solubility (liquidus) line for the protein, but dramatically increases the protein crystal nucleation rate following LLPS, suggesting that the free cysteine has a vital role in suppressing crystallization in the human lens.
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Affiliation(s)
- Alessandro Strofaldi
- Department of Chemistry, Maynooth University, Maynooth, Co. Kildare, Ireland; H. H Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Amir R Khan
- Division of Newborn Medicine, Boston Children's Hospital, Boston, USA; School of Biochemistry, Trinity College Dublin, Ireland
| | - Jennifer J McManus
- H. H Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom.
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Waschbüsch D, Berndsen K, Lis P, Knebel A, Lam YPY, Alessi DR, Khan AR. Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. EMBO Rep 2021; 22:e52675. [PMID: 34580980 PMCID: PMC8567228 DOI: 10.15252/embr.202152675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/16/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022] Open
Abstract
LRRK2 serine/threonine kinase is associated with inherited Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and ImmunologyTrinity College DublinDublin 2Ireland
| | - Kerryn Berndsen
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Yuko PY Lam
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research NetworkChevy ChaseMDUSA
| | - Amir R Khan
- School of Biochemistry and ImmunologyTrinity College DublinDublin 2Ireland
- Division of Newborn MedicineBoston Children's HospitalBostonMAUSA
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6
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Waschbüsch D, Purlyte E, Khan AR. Dual arginine recognition of LRRK2 phosphorylated Rab GTPases. Biophys J 2021; 120:1846-1855. [PMID: 33887226 PMCID: PMC8204342 DOI: 10.1016/j.bpj.2021.03.030] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/01/2022] Open
Abstract
Parkinson's-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime regulators of membrane trafficking in eukaryotic cells. Rabs exert their biological effects by recruitment of effector proteins to subcellular compartments via their Rab-binding domain (RBD). Effectors are modular and typically contain additional domains that regulate various aspects of vesicle formation, trafficking, fusion, and organelle dynamics. The RBD of effectors is typically an α-helical coiled coil that recognizes the GTP conformation of the switch 1 and switch 2 motifs of Rabs. LRRK2 phosphorylates Rab8a at T72 (pT72) of its switch 2 α-helix. This post-translational modification enables recruitment of RILPL2, an effector that regulates ciliogenesis in model cell lines. A newly identified RBD motif of RILPL2, termed the X-cap, has been shown to recognize the phosphate via direct interactions between an arginine residue (R132) and pT72 of Rab8a. Here, we show that a second distal arginine (R130) is also essential for phospho-Rab binding by RILPL2. Through structural, biophysical, and cellular studies, we find that R130 stabilizes the primary R132:pT72 salt bridge through favorable enthalpic contributions to the binding affinity. These findings may have implications for the mechanism by which LRRK2 activation leads to assembly of phospho-Rab complexes and subsequent control of their membrane trafficking functions in cells.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Amir R Khan
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts.
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Rahman SM, Habib A, Khan AR, Ahsan M, Arafat ST, Rahman M, Alsaqufi AS, Mathew RT, Alrashada YN, Alkhamis YA. Cryopreservation Studies on Silver Carp (Hypophthalmichthys molitrix) Embryos. Cryo Letters 2021; 42:178-187. [PMID: 33970996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cryopreservation is an effective tool for the preservation of live biological materials. OBJECTIVE This study examined the suitability of cryopreservation protocols and the effectiveness of ultrasound for silver carp embryos. MATERIALS AND METHODS Embryos at three developmental stages were exposed to 10, 15, 20, and 25% of five cryoprotectants (CPAs), namely propylene glycol (PG), dimethylformamide (DFA), DMSO, MeOH, and ethylene glycol (EG) for 20 min. Embryos were exposed to twelve vitrification solutions (VSs) for 10 (five steps of 2 min), 15 (five steps of 3 min), 20 (five steps of 4 min) min. Embryos were also exposed to ultrasound in VSs prior to cooling for cryopreservation. RESULTS Hatching rates decreased with increasing CPA concentrations while toxicity varied in the order of PG < DMSO < EG < MeOH < DFA. Tail elongation stage was more tolerant to CPA than 6-somites and morula stages. The survival of embryos exposed to ultrasound in VS was remarkably lower than in water. Embryos exposed to ultrasound in VSs under the best conditions did not response well after attempted vitrification. CONCLUSION Ultrasound-mediated CPA impregnation could be effective but other innovative methods may be needed to attain successful cryopreservation.
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Affiliation(s)
- S M Rahman
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh; Fish Resources Research Center, King Faisal University, Hofuf-420, Al-Ahsa, Kingdom of Saudi Arabia.
| | - A Habib
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh
| | - A R Khan
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh
| | - M Ahsan
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh
| | - S T Arafat
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh
| | - M Rahman
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna-9208, Bangladesh
| | - A S Alsaqufi
- 3Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - R T Mathew
- Fish Resources Research Center, King Faisal University, Hofuf-420, Al-Ahsa, Kingdom of Saudi Arabia
| | - Y N Alrashada
- 3Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Y A Alkhamis
- 3Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
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McGrath E, Waschbüsch D, Baker BM, Khan AR. LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain. Small GTPases 2021; 12:133-146. [PMID: 31552791 PMCID: PMC7849779 DOI: 10.1080/21541248.2019.1666623] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/26/2019] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
LRRK2 is a multi-domain Ser/Thr kinase that is associated with inherited and sporadic cases of Parkinson's disease. Many mutations linked to disease are associated within a central ROC-COR regulatory region and the subsequent kinase domain, leading to enhanced catalytic activity. The N-terminus of human LRRK2 consists of armadillo repeat motifs (ARMs) followed by ankyrin repeats (ANKs). Recently, Rab GTPases have emerged as key players in LRRK2 function, both as substrates of the kinase, and as regulators of the catalytic activity. Rabs recruit effector proteins via their GTP-dependent switch 1 and 2 regions to distinct sub-cellular compartments to regulate membrane trafficking. LRRK2 phosphorylates Rab8, Rab10 and Rab12 in switch 2, and this activity is regulated via interactions with Rab29. Furthermore, the related Rab32-subfamily GTPases, Rab32 and Rab38, have also been shown to interact with LRRK2. Here, we have mapped the interactions of the Rab32-subfamily to the ARM domain of LRRK2. The complexes are dependent on the GTP state of the Rabs in vitro, implying that LRRK2 may be an effector of the Rab32-subfamily of small GTPases. X-ray crystal structures of the Rab32-family GTPases and subsequent mutational studies reveal that a positively charged residue in switch 1 is critical for binding of Rab32/38 to LRRK2. Homology modelling and mutational analyses of the ARM domain point to a patch of negatively charged residues that contribute to complex formation. These structural and biochemical studies provide a framework for understanding the molecular basis for Rab regulation of LRRK2 and its role in Parkinson's disease.
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Affiliation(s)
- Emma McGrath
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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Khan W, Nisa NN, Khan AR, Rahbar B, Mehmood SA, Ahmed S, Kamal M, Shah M, Rasool A, Pahanwar WA, Ullah I, Khan S. Roosting ecology and morphometric analysis of Pteropus medius (Indian flying fox) in Lower Dir, district, Pakistan. BRAZ J BIOL 2021; 81:77-82. [PMID: 32401851 DOI: 10.1590/1519-6984.221935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/21/2019] [Indexed: 11/21/2022] Open
Abstract
The present study was conducted to explore morphometric variations of Pteropus medius (the Indian flying fox) and the roosting trees in Lower Dir, Pakistan. The bats were captured from Morus alba, Morus nigra, Brousonetia papyrifera, Pinus raxburghii, Hevea brasiliensis, Platanus orientalis, Populous nigra, Melia azedarach, Eucalyptus camaldulensis and Grevillea robusta through sling shot and mess net methods. A total of 12 bats were studied for the differential morphological features based on age and sex. Male bats were recorded higher in weight than females. The variations were found in body mass (821.1±34.65gm), circumference of body with wings (25.43±0.39cm), wingspan (112.58±1.90cm), Body length (20.73±0.68cm), Snout length (3.42±0.04cm), Eye length (1.45±0.033cm), Length of ear (3.56±0.05cm), Width of ear (2.46±0.04cm), Length b/w ear (5.51±0.11cm), Circumference of neck (12.23±0.24cm), Circumference of body without wings (18.68±0.31cm), Arm wing length (23.2±1.03cm), Length of thumb (5.43±0.1cm), Length of nail (1.89±0.05cm), Hand wing length (29.1±0.51cm), Maximum width of wing (21.03±0.68cm), Length b/w tip of wing to 5th digit (29.39±0.30cm), Length b/w 5th digit to foot (22.97±1.09cm), Length b/w feet (18.31±0.74cm) and Length of foot claw (4.23±0.05cm). This study was designed for analysis of external morphological variations for P. medius (the Indian flying fox) that may help in identification of these bats and their roosting sites.
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Affiliation(s)
- W Khan
- Department of Zoology, University of Malakand, Lower Dir, Pakistan
| | - N N Nisa
- Pakistan Agricultural Research Council, Southern Zone-Agricultural Research Center, Vertebrate Pest Control Institute, University Campus, Karachi, Pakistan
| | - A R Khan
- Department of Zoology, University of Malakand, Lower Dir, Pakistan
| | - B Rahbar
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - S A Mehmood
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - S Ahmed
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - M Kamal
- Department of Zoology, University of Karachi, Karachi-Pakistan
| | - M Shah
- Department of Zoology, University of Swat, Pakistan
| | - A Rasool
- Department of Zoology, University of Swat, Pakistan
| | - W A Pahanwar
- Department of Zoology, Shah Abdul Latif University Khairpur Miris Sindh, Pakistan
| | - I Ullah
- Department of Biological Sciences Karakuram, International University Gilgit, Pakistan
| | - S Khan
- Department of Zoology, University of Malakand, Lower Dir, Pakistan
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Benarroch Y, Juttukonda L, Sabharwal V, Boateng J, Khan AR, Yarrington C, Wachman EM, Taglauer E. Differential Expression of Rab5 and Rab7 Small GTPase Proteins in Placental Tissues From Pregnancies Affected by Maternal Coronavirus Disease 2019. Clin Ther 2021; 43:308-318. [PMID: 33541739 PMCID: PMC7837084 DOI: 10.1016/j.clinthera.2021.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/05/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/26/2022]
Abstract
Purpose The majority of pregnancies affected by maternal coronavirus disease 2019 (COVID-19) do not result in fetal transmission. However, several studies have identified parenchymal changes in their placental tissues, suggesting a placental response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the maternal–fetal interface. Although many COVID-19 placental studies have focused on the expression of the canonical SARS-CoV-2 entry proteins angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2, further characterization of subcellular molecules involved in viral trafficking have not yet been investigated in these tissues. Of interest are Rab proteins, a family of small GTPase proteins that direct intracellular transport between different endocytic organelles. Rab5 and Rab7 in particular have previously been implicated in HIV and cytomegalovirus invasion of placental trophoblast cells in vitro; the localization of these molecules has not been fully characterized within the human maternal–fetal interface, however, or within placental tissues from SARS-CoV-2–infected pregnancies. Methods Using fluorescent immunohistochemistry, Rab5 and Rab7 placental localization and comparative fluorescence intensity were explored in a cohort of placental tissues from pregnancies affected by maternal COVID-19 disease (COVID, n = 15) compared with contemporary control subjects (Control, n = 10). Fluorescence intensity was quantified by using corrected total cell fluorescence values. Findings Within placental villi, Rab5 was consistently localized in syncytiotrophoblast and cytotrophoblast cells. Rab5 had significantly higher mean (SEM) fluorescence intensity in the COVID cohort (Control, 1.96 [0.16]; COVID, 2.62 [0.09]; P = 0.0014). In contrast, although Rab7 was also localized within placental villous syncytiotrophoblast and cytotrophoblast cells, mean (SEM) Rab7 fluorescence intensity was significantly downregulated in COVID vs Control placentas (Control, 35.9 [4.1]; COVID, 20.1 [0.52]; P = 0.0001). Implications This differential expression of Rab5 and Rab7 suggests that placental endocytic pathways may be altered at the maternal–fetal interface in pregnancies affected by maternal SARS-CoV-2 infection. As key molecules governing intracellular vesicle transport, including viral trafficking, Rab GTPase proteins may be of interest for ongoing studies examining placental responses to COVID-19 in pregnancy.
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Affiliation(s)
| | - Lillian Juttukonda
- Boston Combined Residency Program in Pediatrics, Boston Medical Center and Children's Hospital Boston, Boston, MA, USA
| | | | - Jeffery Boateng
- Department of Pediatrics, Boston Medical Center, Boston, MA, USA
| | - Amir R Khan
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | | | - Elisha M Wachman
- Department of Pediatrics, Boston Medical Center, Boston, MA, USA
| | - Elizabeth Taglauer
- Department of Pediatrics, Boston Medical Center, Boston, MA, USA; Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
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11
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Waschbüsch D, Khan AR. Phosphorylation of Rab GTPases in the regulation of membrane trafficking. Traffic 2020; 21:712-719. [PMID: 32969543 PMCID: PMC7756361 DOI: 10.1111/tra.12765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/13/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022]
Abstract
Rab GTPases are master regulators of membrane trafficking in eukaryotic cells. Phosphorylation of Rab GTPases was characterized in the 1990s and there have been intermittent reports of its relevance to Rab functions. Phosphorylation as a regulatory mechanism has gained prominence through the identification of Rabs as physiological substrates of leucine‐rich repeat kinase 2 (LRRK2). LRRK2 is a Ser/Thr kinase that is associated with inherited and sporadic forms of Parkinson disease. In recent years, numerous kinases and their associated signaling pathways have been identified that lead to phosphorylation of Rabs. These emerging studies suggest that serine/threonine and tyrosine phosphorylation of Rabs may be a widespread and under‐appreciated mechanism for controlling their membrane trafficking functions. Here we survey current knowledge of Rab phosphorylation and discuss models for how this post‐translational mechanism exerts control of membrane trafficking.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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12
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Waschbüsch D, Purlyte E, Pal P, McGrath E, Alessi DR, Khan AR. Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2. Structure 2020; 28:406-417.e6. [PMID: 32017888 PMCID: PMC7139218 DOI: 10.1016/j.str.2020.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
Rab8a is associated with the dynamic regulation of membrane protrusions in polarized cells. Rab8a is one of several Rab GTPases that are substrates of leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase that is linked to Parkinson's disease. Rab8a is phosphorylated at T72 (pT72) in its switch 2 helix and recruits the phospho-specific effector RILPL2, which subsequently regulates ciliogenesis. Here, we report the crystal structure of phospho-Rab8a (pRab8a) in complex with the RH2 (RILP homology) domain of RILPL2. The complex is a heterotetramer with RILPL2 forming a central α-helical dimer that bridges two pRab8a molecules. The N termini of the α helices cross over, forming an X-shaped cap (X-cap) that orients Arg residues from RILPL2 toward pT72. X-cap residues critical for pRab8a binding are conserved in JIP3 and JIP4, which also interact with LRRK2-phosphorylated Rab10. We propose a general mode of recognition for phosphorylated Rab GTPases by this family of phospho-specific effectors.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Prosenjit Pal
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emma McGrath
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland; Division of Newborn Medicine, Boston Children's Hospital, Boston, USA.
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13
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Altan I, Khan AR, James S, Quinn MK, McManus JJ, Charbonneau P. Using Schematic Models to Understand the Microscopic Basis for Inverted Solubility in γD-Crystallin. J Phys Chem B 2019; 123:10061-10072. [PMID: 31557434 DOI: 10.1021/acs.jpcb.9b07774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inverted solubility-melting a crystal by cooling-is observed in a handful of proteins, such as carbomonoxy hemoglobin C and γD-crystallin. In human γD-crystallin, the phenomenon is associated with the mutation of the 23rd residue, a proline, to a threonine, serine, or valine. One proposed microscopic mechanism entails an increase in surface hydrophobicity upon mutagenesis. Recent crystal structures of a double mutant that includes the P23T mutation allow for a more careful investigation of this proposal. Here, we first measure the surface hydrophobicity of various mutant structures of γD-crystallin and discern no notable increase in hydrophobicity upon mutating the 23rd residue. We then investigate the solubility inversion regime with a schematic patchy particle model that includes one of three variants of temperature-dependent patch energies: two of the hydrophobic effect, and one of a more generic nature. We conclude that, while solubility inversion due to the hydrophobic effect may be possible, microscopic evidence to support it in γD-crystallin is weak. More generally, we find that solubility inversion requires a fine balance between patch strengths and their temperature-dependent component, which may explain why inverted solubility is not commonly observed in proteins. We also find that the temperature-dependent interaction has only a negligible impact on liquid-liquid phase boundaries of γD-crystallin, in line with previous experimental observations.
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Affiliation(s)
| | - Amir R Khan
- School of Biochemistry and Immunology , Trinity College Dublin , Dublin , Ireland
| | - Susan James
- Department of Chemistry , Maynooth University , Maynooth , Ireland
| | - Michelle K Quinn
- Department of Chemistry , Maynooth University , Maynooth , Ireland
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14
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Khan AR, James S, Quinn MK, Altan I, Charbonneau P, McManus JJ. Temperature-Dependent Interactions Explain Normal and Inverted Solubility in a γD-Crystallin Mutant. Biophys J 2019; 117:930-937. [PMID: 31422822 DOI: 10.1016/j.bpj.2019.07.019] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/30/2022] Open
Abstract
Protein crystal production is a major bottleneck in the structural characterization of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of the protein surface, due to the variety of amino-acid side chains in contact with solvent, contributes to protein-protein contact formation in the crystal lattice is a major obstacle to predicting and optimizing crystallization. The relative scarcity of sophisticated theoretical models that include sufficient detail to link collective behavior, captured in protein phase diagrams, and molecular-level details, determined from high-resolution structural information, is a further barrier. Here, we present two crystal structures for the P23T + R36S mutant of γD-crystallin, each with opposite solubility behavior: one melts when heated, the other when cooled. When combined with the protein phase diagram and a tailored patchy particle model, we show that a single temperature-dependent interaction is sufficient to stabilize the inverted solubility crystal. This contact, at the P23T substitution site, relates to a genetic cataract and reveals at a molecular level the origin of the lowered and retrograde solubility of the protein. Our results show that the approach employed here may present a productive strategy for the rationalization of protein crystallization.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Susan James
- Department of Chemistry, Maynooth University, Maynooth, Ireland
| | | | - Irem Altan
- Department of Chemistry, Duke University, Durham, North Carolina
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15
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Garg RR, Jackson CB, Rahman MM, Khan AR, Lewin AS, McFadden G. Myxoma virus M013 protein antagonizes NF-κB and inflammasome pathways via distinct structural motifs. J Biol Chem 2019; 294:8480-8489. [PMID: 30940649 DOI: 10.1074/jbc.ra118.006040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 09/28/2018] [Revised: 02/12/2019] [Indexed: 12/16/2022] Open
Abstract
Among the repertoire of immunoregulatory proteins encoded by myxoma virus, M013 is a viral homologue of the viral pyrin domain-only protein (vPOP) family. In myeloid cells, M013 protein has been shown to inhibit both the inflammasome and NF-κB signaling pathways by direct binding to ASC1 and NF-κB1, respectively. In this study, a three-dimensional homology model of the M013 pyrin domain (PYD) was built based on similarities to known PYD structures. A distinctive feature of the deduced surface electrostatic map of the M013 PYD is the presence of a negatively region consisting of numerous aspartate and glutamate residues in close proximity. Single-site mutations of aspartate and glutamate residues reveal their role in interactions with ASC-1. The biological significance of charge complementarity in the M013-ASC-1 interaction was further confirmed by functional assays of caspase-1 activation and subsequent secretion of cytokines. M013 also has a unique 33-residue C-terminal tail that follows the N-terminal PYD, and it is enriched in positively charged residues. Deletion of the tail of M013 significantly inhibited the interactions between M013 and NF-κB1, thus compromising the ability of the viral protein to suppress the secretion of pro-inflammatory cytokines. These results demonstrate that vPOP M013 exploits distinct structural motifs to regulate both the inflammasome and NF-κB pathways.
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Affiliation(s)
- Rekha R Garg
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611
| | - Cody B Jackson
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611
| | - Masmudur M Rahman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611; Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute, Arizona State University, Tempe, Arizona 85281
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
| | - Alfred S Lewin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611.
| | - Grant McFadden
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611; Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute, Arizona State University, Tempe, Arizona 85281.
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16
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Waschbüsch D, Hübel N, Ossendorf E, Lobbestael E, Baekelandt V, Lindsay AJ, McCaffrey MW, Khan AR, Barnekow A. Rab32 interacts with SNX6 and affects retromer-dependent Golgi trafficking. PLoS One 2019; 14:e0208889. [PMID: 30640902 PMCID: PMC6331118 DOI: 10.1371/journal.pone.0208889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022] Open
Abstract
The Rab family of small GTPases regulate various aspects of cellular dynamics in eukaryotic cells. Membrane trafficking has emerged as central to the functions of leucine-rich repeat kinase 2 (LRRK2), which is associated with inherited and sporadic forms of Parkinson's disease (PD). Rabs act as both regulators of the catalytic activity and targets for serine/threonine phosphorylation by LRRK2. Rab32, Rab38 and Rab29 have been shown to regulate LRRK2 sub-cellular localization through direct interactions. Recently, Rab29 was shown to escort LRRK2 to the Golgi apparatus and activate the phosphorylation of Rab8 and Rab10. Rab32 is linked to multiple cellular functions including endosomal trafficking, mitochondrial dynamics, and melanosome biogenesis. A missense mutation in Rab32 has also recently been linked to PD. Here, we demonstrate that Rab32 directly interacts with sorting nexin 6 (SNX6). SNX6 is a transient subunit of the retromer, an endosome-Golgi retrieval complex whose Vps35 subunit is strongly associated with PD. We could further show that localization of cation-independent mannose-6-phosphate receptors, which are recycled to the trans-Golgi network (TGN) by the retromer, was affected by both Rab32 and SNX6. These data imply that Rab32 is linked to SNX6/retromer trafficking at the Golgi, and also suggests a possible connection between the retromer and Rab32 in the trafficking and biological functions of LRRK2.
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Affiliation(s)
- Dieter Waschbüsch
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Nicole Hübel
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
| | - Edith Ossendorf
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
| | - Evy Lobbestael
- Laboratory for Neurobiology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, KU Leuven, Leuven, Belgium
| | - Andrew J. Lindsay
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Mary W. McCaffrey
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- * E-mail: (AK); (AB)
| | - Angelika Barnekow
- Department of Experimental Tumorbiology, Westfalische Wilhelms University Muenster, Muenster, Germany
- * E-mail: (AK); (AB)
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17
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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18
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018; 57:7126-7130. [DOI: 10.1002/anie.201803232] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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20
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Mulvaney EP, O'Meara F, Khan AR, O'Connell DJ, Kinsella BT. Identification of α-helix 4 (α4) of Rab11a as a novel Rab11-binding domain (RBD): Interaction of Rab11a with the Prostacyclin Receptor. Biochim Biophys Acta Mol Cell Res 2017; 1864:1819-1832. [PMID: 28739266 DOI: 10.1016/j.bbamcr.2017.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/28/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
The cellular trafficking of numerous G protein-coupled receptors (GPCRs) is known to be regulated by Rab proteins that involves a direct protein:protein interaction between the receptor and the GTPase. In the case of the human prostacyclin receptor (hIP), it undergoes agonist-induced internalization and subsequent Rab11a-dependent recyclization involving an interaction between a Rab11-binding domain (RBD) localized within its carboxyl-tail domain with Rab11a. However, the GPCR-interacting domain on Rab11a itself is unknown. Hence, we sought to identify the region within Rab11a that mediates its interaction with the RBD of the hIP. The α4 helix region of Rab11 was identified as a novel binding domain for the hIP, a site entirely distinct from the Switch I/Switch II -regions that act as specific binding domain for most other Rab and Ras-like GTPase interactants. Specifically, Glu138 within α4 helix of Rab11a appears to contact with key residues (e.g. Lys304) within the RBD of the hIP, where such contacts differ depending on the agonist-activated versus -inactive status of the hIP. Through mutational studies, supported by in silico homology modelling of the inactive and active hIP:Rab11a complexes, a mechanism is proposed to explain both the constitutive and agonist-induced binding of Rab11a to regulate intracellular trafficking of the hIP. Collectively, these studies are not only the first to identify α4 helix of Rab11a as a protein binding domain on the GTPase but also reveal novel mechanistic insights into the intracellular trafficking of the hIP, and potentially of other members of the GPCR superfamily, involving Rab11-dependent mechanisms.
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Affiliation(s)
- Eamon P Mulvaney
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - David J O'Connell
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - B Therese Kinsella
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.
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James MNG, Fraser ME, Khan AR, Parrish JC, Smith WW, Bartlett PA. Structural studies of conformationally-restricted ligands binding to aspartic peptidases. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317099834] [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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22
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Javaid A, Hasan R, Zafar A, Chaudry MA, Qayyum S, Qadeer E, Shaheen Z, Agha N, Rizvi N, Afridi MZ, Chima MK, Khan AR, Ghafoor A, Khan S, Awan SR, Akhtar S, Choudry K, Iqbal ZH, Ansarie M, Ahmad N. Pattern of first- and second-line drug resistance among pulmonary tuberculosis retreatment cases in Pakistan. Int J Tuberc Lung Dis 2017; 21:303-308. [PMID: 28225340 DOI: 10.5588/ijtld.16.0444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drug resistance in general, and multidrug-resistant tuberculosis (MDR-TB) in particular, threatens global tuberculosis (TB) control efforts. Population-based estimates of drug resistance are needed to develop strategies for controlling drug-resistant TB in Pakistan. OBJECTIVE To obtain population-based data on Mycobacterium tuberculosis drug resistance in Pakistan. METHODS To obtain drug resistance data, we conducted a population-based study of TB cases in all provinces of Pakistan. We performed culture and drug susceptibility testing on M. tuberculosis isolates from patients with a prior history of anti-tuberculosis treatment (retreatment cases) from all over the country. RESULTS Of 544 isolates from previously treated cases, 289 (53.1%) were susceptible to all first-line drugs, 255 (46.9%) were resistant to at least one anti-tuberculosis drug and 132 (24.3%) were MDR-TB. Among MDR-TB isolates, 47.0% were ofloxacin (OFX) resistant. Extensively drug-resistant TB was found in two (0.4%) isolates. CONCLUSION Prevalence of drug resistance in retreatment isolates was high. The alarmingly high prevalence of OFX resistance among MDR-TB isolates may threaten the success of efforts to control and treat MDR-TB.
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Affiliation(s)
- A Javaid
- Department of Pulmonology, Postgraduate Medical Institute, Lady Reading Hospital, Peshawar
| | - R Hasan
- Department of Microbiology, Agha Khan University, Karachi
| | - A Zafar
- Department of Microbiology, Agha Khan University, Karachi
| | | | - S Qayyum
- Ojha Institute of Chest Disease, Karachi
| | - E Qadeer
- National TB Control Programme, Islamabad
| | - Z Shaheen
- Department of Pulmonology, Nishtar Medical College, Multan
| | - N Agha
- Fatima Jinnah Chest Hospital, Quetta
| | - N Rizvi
- Department of Chest Medicine, Jinnah Postgraduate Medical Centre, Karachi
| | | | - M K Chima
- Department of Pulmonology, Services Hospital, Lahore
| | - A R Khan
- Department of Pulmonology, Ayub Medical College, Abbottabad
| | | | - S Khan
- Department of Chest Medicine, Lahore General Hospital, Lahore
| | | | - S Akhtar
- Department of Medicine, Ziauddin University, Karachi
| | - K Choudry
- Department of Pulmonology, King Edward Medical University, Lahore
| | - Z H Iqbal
- Department of Pulmonology, Allama Iqbal Medical College, Lahore
| | - M Ansarie
- Orthopaedic and Medical Institute, Karachi, Pakistan
| | - N Ahmad
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
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Willis-Fox N, Gutacker A, Browne MP, Khan AR, Lyons MEG, Scherf U, Evans RC. Selective recognition of biologically important anions using a diblock polyfluorene–polythiophene conjugated polyelectrolyte. Polym Chem 2017. [DOI: 10.1039/c7py01478c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorescence detection of nucleotide phosphates with a polyfluorene–polythiophene diblock copolymer is demonstrated, accompanied by determination of the sensor mechanism.
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Affiliation(s)
- Niamh Willis-Fox
- School of Chemistry and CRANN
- Trinity College Dublin
- The University of Dublin
- Ireland
| | - Andrea Gutacker
- Macromolecular Chemistry Group (buwmakro) and Institute for Polymer Technology
- Bergische Universität Wuppertal
- 42119 Wuppertal
- Germany
| | - Michelle P. Browne
- School of Chemistry and CRANN
- Trinity College Dublin
- The University of Dublin
- Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology
- University of Dublin
- Trinity College Dublin
- The University of Dublin
- Dublin 2
| | - Michael E. G. Lyons
- School of Chemistry and CRANN
- Trinity College Dublin
- The University of Dublin
- Ireland
| | - Ullrich Scherf
- Macromolecular Chemistry Group (buwmakro) and Institute for Polymer Technology
- Bergische Universität Wuppertal
- 42119 Wuppertal
- Germany
| | - Rachel C. Evans
- School of Chemistry and CRANN
- Trinity College Dublin
- The University of Dublin
- Ireland
- Department of Materials Science and Metallurgy
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24
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Khan AR, Al-Awadi L, Al-Rashidi MS. Control of ammonia and urea emissions from urea manufacturing facilities of Petrochemical Industries Company (PIC), Kuwait. J Air Waste Manag Assoc 2016; 66:609-618. [PMID: 26828877 DOI: 10.1080/10962247.2016.1145154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED Petrochemical Industries Company (PIC) in Kuwait has mitigated the pollution problem of ammonia and urea dust by replacing the melting and prilling units of finished-product urea prills with an environmentally friendly granulation process. PIC has financed a research project conducted by the Coastal and Air Pollution Program's research staff at the Kuwait Institute for Scientific Research to assess the impact of pollution control strategies implemented to maintain a healthy productive environment in and around the manufacturing premises. The project was completed in three phases: the first phase included the pollution monitoring of the melting and prilling units in full operation, the second phase covered the complete shutdown period where production was halted completely and granulation units were installed, and the last phase encompassed the current modified status with granulation units in full operation. There was substantial decrease in ammonia emissions, about 72%, and a 52.7% decrease in urea emissions with the present upgrading of old melting and prilling units to a state-of-the-art technology "granulation process" for a final finished product. The other pollutants, sulfur dioxide (SO2), nitrogen oxides (NOx), and volatile organic compounds (VOCs), have not shown any significant change, as the present modification has not affected the sources of these pollutants. IMPLICATIONS Petrochemical Industries Company (PIC) in Kuwait has ammonia urea industries, and there were complaints about ammonia and urea dust pollution. PIC has resolved this problem by replacing "melting and prilling unit" of final product urea prills by more environmentally friendly "granulation unit." Environmental Pollution and Climate Program has been assigned the duty of assessing the outcome of this change and how that influenced ammonia and urea dust emissions from the urea manufacturing plant.
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Affiliation(s)
- A R Khan
- a Environmental Pollution and Climate Program, Environment and Life Sciences Research Center , Kuwait Institute for Scientific Research , Safat , Kuwait
| | - L Al-Awadi
- a Environmental Pollution and Climate Program, Environment and Life Sciences Research Center , Kuwait Institute for Scientific Research , Safat , Kuwait
| | - M S Al-Rashidi
- a Environmental Pollution and Climate Program, Environment and Life Sciences Research Center , Kuwait Institute for Scientific Research , Safat , Kuwait
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25
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Oliveira T, Sharkey MA, Engel PC, Khan AR. Crystal structure of a chimaeric bacterial glutamate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2016; 72:462-6. [PMID: 27303899 PMCID: PMC4909246 DOI: 10.1107/s2053230x16007305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/02/2016] [Indexed: 11/10/2022] Open
Abstract
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)(+) as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD(+) versus NADP(+), but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase from Clostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia coli enzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP(+) cofactor from the parent E. coli domain II, although there are subtle differences in catalytic activity.
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Affiliation(s)
- Tânia Oliveira
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
| | - Michael A. Sharkey
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul C. Engel
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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26
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Lall P, Lindsay AJ, Hanscom S, Kecman T, Taglauer ES, McVeigh UM, Franklin E, McCaffrey MW, Khan AR. Structure-Function Analyses of the Interactions between Rab11 and Rab14 Small GTPases with Their Shared Effector Rab Coupling Protein (RCP). J Biol Chem 2015; 290:18817-32. [PMID: 26032412 DOI: 10.1074/jbc.m114.612366] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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: 10/15/2014] [Indexed: 01/05/2023] Open
Abstract
Rab GTPases recruit effector proteins, via their GTP-dependent switch regions, to distinct subcellular compartments. Rab11 and Rab25 are closely related small GTPases that bind to common effectors termed the Rab11 family of interacting proteins (FIPs). The FIPs are organized into two subclasses (class I and class II) based on sequence and domain organization, and both subclasses contain a highly conserved Rab-binding domain at their C termini. Yeast two-hybrid and biochemical studies have revealed that the more distantly related Rab14 also interacts with class I FIPs. Here, we perform detailed structural, thermodynamic, and cellular analyses of the interactions between Rab14 and one of the class I FIPs, the Rab-coupling protein (RCP), to clarify the molecular aspects of the interaction. We find that Rab14 indeed binds to RCP, albeit with reduced affinity relative to conventional Rab11-FIP and Rab25-FIP complexes. However, in vivo, Rab11 recruits RCP onto biological membranes. Furthermore, biophysical analyses reveal a noncanonical 1:2 stoichiometry between Rab14-RCP in dilute solutions, in contrast to Rab11/25 complexes. The structure of Rab14-RCP reveals that Rab14 interacts with the canonical Rab-binding domain and also provides insight into the unusual properties of the complex. Finally, we show that both the Rab coupling protein and Rab14 function in neuritogenesis.
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Affiliation(s)
- Patrick Lall
- From the School of Biochemistry and Immunology, Trinity College, Dublin 2 and
| | - Andrew J Lindsay
- the Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Sara Hanscom
- the Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Tea Kecman
- From the School of Biochemistry and Immunology, Trinity College, Dublin 2 and
| | | | - Una M McVeigh
- From the School of Biochemistry and Immunology, Trinity College, Dublin 2 and
| | - Edward Franklin
- From the School of Biochemistry and Immunology, Trinity College, Dublin 2 and
| | - Mary W McCaffrey
- the Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Amir R Khan
- From the School of Biochemistry and Immunology, Trinity College, Dublin 2 and
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27
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Mariño RJ, Khan AR, Tham R, Khew CW, Stevenson C. Pattern and factors associated with utilization of dental services among older adults in rural Victoria. Aust Dent J 2014; 59:504-10. [DOI: 10.1111/adj.12216] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2014] [Indexed: 11/29/2022]
Affiliation(s)
- RJ Mariño
- Oral Health Cooperative Research Centre; Melbourne Dental School; The University of Melbourne; Victoria
| | - AR Khan
- Oral Health Cooperative Research Centre; Melbourne Dental School; The University of Melbourne; Victoria
| | - R Tham
- School of Rural Health; Monash University; Victoria
| | - C-W Khew
- Bendigo Health Care Group; Victoria
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28
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Khan AR, Ménétrey J. Structural biology of Arf and Rab GTPases' effector recruitment and specificity. Structure 2014; 21:1284-97. [PMID: 23931141 DOI: 10.1016/j.str.2013.06.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/30/2013] [Accepted: 06/05/2013] [Indexed: 11/15/2022]
Abstract
Arf and Rab proteins, members of small GTPases superfamily, localize to specific subcellular compartments and regulate intracellular trafficking. To carry out their cellular functions, Arfs/Rabs interact with numerous and structurally diverse effector proteins. Over the years, a number of Arf/Rab:effector complexes have been crystallized and their structures reveal shared binding modes including α-helical packing, β-β complementation, and heterotetrameric assemblies. We review available structural information and provide a framework for in-depth analysis of complexes. The unifying features that we identify are organized into a classification scheme for different modes of Arf/Rab:effector interactions, which includes "all-α-helical," "mixed α-helical," "β-β zipping," and "bivalent" modes of binding. Additionally, we highlight structural determinants that are the basis of effector specificity. We conclude by expanding on functional implications that are emerging from available structural information under our proposed classification scheme.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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29
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Stack J, Hurst TP, Flannery SM, Brennan K, Rupp S, Oda SI, Khan AR, Bowie AG. Poxviral protein A52 stimulates p38 mitogen-activated protein kinase (MAPK) activation by causing tumor necrosis factor receptor-associated factor 6 (TRAF6) self-association leading to transforming growth factor β-activated kinase 1 (TAK1) recruitment. J Biol Chem 2013; 288:33642-33653. [PMID: 24114841 DOI: 10.1074/jbc.m113.485490] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Vaccinia virus encodes a number of proteins that inhibit and manipulate innate immune signaling pathways that also have a role in virulence. These include A52, a protein shown to inhibit IL-1- and Toll-like receptor-stimulated NFκB activation, via interaction with interleukin-1 receptor-associated kinase 2 (IRAK2). Interestingly, A52 was also found to activate p38 MAPK and thus enhance Toll-like receptor-dependent IL-10 induction, which was TRAF6-dependent, but the manner in which A52 manipulates TRAF6 to stimulate p38 activation was unclear. Here, we show that A52 has a non-canonical TRAF6-binding motif that is essential for TRAF6 binding and p38 activation but dispensable for NFκB inhibition and IRAK2 interaction. Wild-type A52, but not a mutant defective in p38 activation and TRAF6 binding (F154A), caused TRAF6 oligomerization and subsequent TRAF6-TAK1 association. The crystal structure of A52 shows that it adopts a Bcl2-like fold and exists as a dimer in solution. Residue Met-65 was identified as being located in the A52 dimer interface, and consistent with that, A52-M65E was impaired in its ability to dimerize. A52-M65E although capable of interacting with TRAF6, was unable to cause either TRAF6 self-association, induce the TRAF6-TAK1 association, or activate p38 MAPK. The results suggest that an A52 dimer causes TRAF6 self-association, leading to TAK1 recruitment and p38 activation. This reveals a molecular mechanism whereby poxviruses manipulate TRAF6 to activate MAPKs (which can be proviral) without stimulating antiviral NFκB activation.
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Affiliation(s)
- Julianne Stack
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Tara P Hurst
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sinead M Flannery
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Kiva Brennan
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sebastian Rupp
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Shun-Ichiro Oda
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Amir R Khan
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Andrew G Bowie
- Immunology Research Centre, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland.
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30
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Lall P, Horgan CP, Oda S, Franklin E, Sultana A, Hanscom SR, McCaffrey MW, Khan AR. Structural and functional analysis of FIP2 binding to the endosome-localised Rab25 GTPase. Biochim Biophys Acta 2013; 1834:2679-90. [PMID: 24056041 DOI: 10.1016/j.bbapap.2013.09.005] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/08/2013] [Accepted: 09/12/2013] [Indexed: 11/30/2022]
Abstract
Rab small GTPases are the master regulators of intracellular trafficking in eukaryotes. They mediate spatial and temporal recruitment of effector proteins to distinct cellular compartments through GTP-induced changes in their conformation. Despite numerous structural studies, the molecular basis for Rab/effector specificity and subsequent biological activity remains poorly understood. Rab25, also known as Rab11c, which is epithelial-specific, has been heavily implicated in ovarian cancer development and independently appears to act as a tumour suppressor in the context of a distinct subset of carcinomas. Here, we show that Rab25 associates with FIP2 and can recruit this effector protein to endosomal membranes. We report the crystal structure of Rab25 in complex with the C-terminal region of FIP2, which consists of a central dimeric FIP2 coiled-coil that mediates a heterotetrameric Rab25-(FIP2)2-Rab25 complex. Thermodynamic analyses show that, despite a relatively conserved interface, FIP2 binds to Rab25 with an approximate 3-fold weaker affinity than to Rab11a. Reduced affinity is mainly associated with lower enthalpic gains for Rab25:FIP2 complex formation, and can be attributed to subtle differences in the conformations of switch 1 and switch 2. These cellular, structural and thermodynamic studies provide insight into the Rab11/Rab25 subfamily of small GTPases that regulate endosomal trafficking pathways in eukaryotes.
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Affiliation(s)
- Patrick Lall
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
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31
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Lindsay AJ, Jollivet F, Horgan CP, Khan AR, Raposo G, McCaffrey MW, Goud B. Identification and characterization of multiple novel Rab-myosin Va interactions. Mol Biol Cell 2013; 24:3420-34. [PMID: 24006491 PMCID: PMC3814135 DOI: 10.1091/mbc.e13-05-0236] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [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] [Indexed: 12/16/2022] Open
Abstract
A systematic screen of the entire human Rab GTPase family for interactions with myosin Va identified 10 novel Rab partners for myosin Va, all of which belong to the endocytic recycling and post-Golgi secretory membrane network. However, Rab10 and Rab11 appear to be the major determinants of its recruitment to intracellular membranes. Myosin Va is a widely expressed actin-based motor protein that binds members of the Rab GTPase family (3A, 8A, 10, 11A, 27A) and is implicated in many intracellular trafficking processes. To our knowledge, myosin Va has not been tested in a systematic screen for interactions with the entire Rab GTPase family. To that end, we report a yeast two-hybrid screen of all human Rabs for myosin Va-binding ability and reveal 10 novel interactions (3B, 3C, 3D, 6A, 6A′, 6B, 11B, 14, 25, 39B), which include interactions with three new Rab subfamilies (Rab6, Rab14, Rab39B). Of interest, myosin Va interacts with only a subset of the Rabs associated with the endocytic recycling and post-Golgi secretory systems. We demonstrate that myosin Va has three distinct Rab-binding domains on disparate regions of the motor (central stalk, an alternatively spliced exon, and the globular tail). Although the total pool of myosin Va is shared by several Rabs, Rab10 and Rab11 appear to be the major determinants of its recruitment to intracellular membranes. We also present evidence that myosin Va is necessary for maintaining a peripheral distribution of Rab11- and Rab14-positive endosomes.
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Affiliation(s)
- Andrew J Lindsay
- Molecular Cell Biology Laboratory, School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland Centre de Recherche, Molecular Mechanisms of Intracellular Transport, Institut Curie, CNRS UMR144, F-75248 Paris, France School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland Structure and Membrane Compartments, Institut Curie, CNRS UMR144, F-75248 Paris, France Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, CNRS UMR144, F-75248 Paris, France
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Sharkey MA, Oliveira TF, Engel PC, Khan AR. Structure of NADP(+)-dependent glutamate dehydrogenase from Escherichia coli--reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases. FEBS J 2013; 280:4681-92. [PMID: 23879525 DOI: 10.1111/febs.12439] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 11/26/2022]
Abstract
Glutamate dehydrogenases (GDHs; EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate, using NAD(+) and/or NADP(+) as a cofactor. Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding domain I followed by a nucleotide-binding domain II. The reaction occurs in a catalytic cleft between the two domains. Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the GDH family remains poorly understood. Here, the refined crystal structure of Escherichia coli GDH in the absence of reactants is described at 2.5-Å resolution. Modelling of NADP(+) in domain II reveals the potential contribution of positively charged residues from a neighbouring α-helical hairpin to phosphate recognition. In addition, a serine that follows the P7 aspartate is presumed to form a hydrogen bond with the 2'-phosphate. Mutagenesis and kinetic analysis confirms the importance of these residues in NADP(+) recognition. Surprisingly, one of the positively charged residues is conserved in all sequences of NAD(+)-dependent enzymes, but the conformations adopted by the corresponding regions in proteins whose structure has been solved preclude their contribution to the coordination of the 2'-ribose phosphate of NADP(+). These studies clarify the sequence-structure relationships in bacterial GDHs, revealing that identical residues may specify different coenzyme preferences, depending on the structural context. Primary sequence alone is therefore not a reliable guide for predicting coenzyme specificity. We also consider how it is possible for a single sequence to accommodate both coenzymes in the dual-specificity GDHs of animals.
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Affiliation(s)
- Michael A Sharkey
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Ireland
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Paterson AL, Sut MK, Khan AR, Sharma HK. Prostatic biopsies in selected men aged 75 years and older guide key clinical management decisions. Int Urol Nephrol 2013; 45:1539-44. [PMID: 23896941 DOI: 10.1007/s11255-013-0506-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/24/2013] [Indexed: 12/01/2022]
Abstract
PURPOSE Increasing life expectancy and PSA testing has increased the number of men over the age of seventy-five presenting for investigation of potential prostate malignancies. Prostatic biopsies provide diagnostic information; however, they are invasive and may not alter management decisions. Therefore, this study aimed to investigate whether prostate biopsies in this age group were justified. MATERIALS AND METHODS All men aged 75 years and older who underwent prostatic biopsies between January 2010 and November 2011 at Bedford Hospital were identified and the indication for the biopsies, histopathological results and subsequent management plan investigated. RESULTS One hundred and thirty-eight (138) prostatic biopsies were undertaken and malignancies identified in 60/138 (43 %) cases. Prebiopsy PSA and examination findings had a poor positive predictive value of 54 %. Fifty-five out of sixty (92 %) cancers were classified as high or medium risk disease with 30/60 (50 %) patients commencing radiotherapy treatment with curative intent. CONCLUSION In selected patients aged 75 years or over, prostatic biopsies provide important diagnostic information which directly impacts on clinical decisions, supporting their use in this age group.
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Affiliation(s)
- A L Paterson
- Department of Urology, Bedford Hospital, Bedford, UK
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34
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Affiliation(s)
- L Barreto
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK
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35
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Mariño RJ, Khan AR, Morgan M. Systematic review of publications on economic evaluations of caries prevention programs. Caries Res 2013; 47:265-72. [PMID: 23407213 DOI: 10.1159/000346917] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 12/29/2012] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to perform a systematic review of economic evaluations (EEs) of dental caries prevention programs to objectively retrieve, synthesize and describe available information on the field. Several strategies were combined to search for literature published between January 1975 and April 2012. MEDLINE, EconoLit and ISI formed the basis of the literature search. The study selection was done using predefined inclusion and exclusion criteria. Bibliographic listings of all retrieved articles were hand-searched. The search identified 206 references. An evaluative framework was developed based on the Centre for Reviews and Dissemination's 'Guidance for undertaking reviews in health care' (York University, 2009). Background information included publication vehicle, year of publication, geographic focus, type of preventive program and type of economic analysis. 63 studies were included in the review. The most common preventive strategies evaluated were dental sealants (n = 13), water fluoridation (n = 12) and mixed interventions (n = 12). By type of EE undertaken, 30 were cost-effectiveness analyses, 22 were cost-benefit analyses, and 5 presented both cost-effectiveness and cost-benefit analyses. Few studies were cost-utility analyses (n = 5) or cost minimization analyses (n = 2). By year of publication, most were published after 2003. The review revealed that, although the number of publications reporting EEs has increased significantly in recent years, the quality of the reporting needs to be improved. The main methodological problems identified in the review were the limited information provided on adjustments for discounting in addition to inadequate sensitivity analyses. Attention also needs to be given to the analysis and interpretation of the results of the EEs.
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Affiliation(s)
- R J Mariño
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of Melbourne, Melbourne, Vic., Australia.
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36
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Abstract
Rabs comprise the largest member of the Ras superfamily of small GTPases with over 60 proteins in mammals and 11 proteins in yeast. Like all small GTPases, Rabs oscillate between an inactive GDP-bound conformation and an active GTP-bound state that is tethered to lipid membranes via a C-terminal prenylation site on conserved cysteine residues. In their active state, Rabs regulate various aspects of membrane trafficking, including vesicle formation, transport, docking, and fusion. The critical element of biological activity is the recruitment of cytosolic effector proteins to specific endomembranes by active Rabs. The importance of Rabs in cellular processes is apparent from their links to genetic disorders, immunodeficiency, cancer, and pathogen invasion. During the last decade, numerous structures of complexes have shed light on the molecular basis for Rab/effector specificity and their topological organization on subcellular membranes. Here, I review the known structures of Rab/effector complexes and their modes of oligomerization. This is followed by a brief discussion on the thermodynamics of effector recruitment, which has not been documented sufficiently in previous reviews. A summary of diseases associated with Rab/effector trafficking pathways concludes this chapter.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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Franklin E, Khan AR. Poxvirus antagonism of innate immunity by Bcl-2 fold proteins. J Struct Biol 2013; 181:1-10. [DOI: 10.1016/j.jsb.2012.10.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/28/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
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38
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Braulik GT, Bhatti ZI, Ehsan T, Hussain B, Khan AR, Khan A, Khan U, Kundi KU, Rajput R, Reichert AP, Northridge SP, Bhagat HB, Garstang R. Robust abundance estimate for endangered river dolphin subspecies in South Asia. ENDANGER SPECIES RES 2012. [DOI: 10.3354/esr00425] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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39
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McGovern RE, Fernandes H, Khan AR, Power NP, Crowley PB. Protein camouflage in cytochrome c–calixarene complexes. Nat Chem 2012; 4:527-33. [DOI: 10.1038/nchem.1342] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/22/2012] [Indexed: 01/06/2023]
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40
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Fernandes H, Franklin E, Jollivet F, Bliedtner K, Khan AR. Mapping the interactions between a RUN domain from DENND5/Rab6IP1 and sorting nexin 1. PLoS One 2012; 7:e35637. [PMID: 22558185 PMCID: PMC3338420 DOI: 10.1371/journal.pone.0035637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/19/2012] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic cells have developed a diverse repertoire of Rab GTPases to regulate vesicle trafficking pathways. Together with their effector proteins, Rabs mediate various aspects of vesicle formation, tethering, docking and fusion, but details of the biological roles elicited by effectors are largely unknown. Human Rab6 is involved in the trafficking of vesicles at the level of Golgi via interactions with numerous effector proteins. We have previously determined the crystal structure of Rab6 in complex with DENND5, alternatively called Rab6IP1, which comprises two RUN domains (RUN1 and RUN2) separated by a PLAT domain. The structure of Rab6/RUN1-PLAT (Rab6/R1P) revealed the molecular basis for Golgi recruitment of DENND5 via the RUN1 domain, but the functional role of the RUN2 domain has not been well characterized. Here we show that a soluble DENND5 construct encompassing the RUN2 domain binds to the N-terminal region of sorting nexin 1 by surface plasmon resonance analyses.
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Affiliation(s)
| | - Edward Franklin
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Florence Jollivet
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | | | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
- * E-mail:
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Jin Y, Sultana A, Gandhi P, Franklin E, Hamamoto S, Khan AR, Munson M, Schekman R, Weisman LS. Myosin V transports secretory vesicles via a Rab GTPase cascade and interaction with the exocyst complex. Dev Cell 2012; 21:1156-70. [PMID: 22172676 DOI: 10.1016/j.devcel.2011.10.009] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 08/26/2011] [Accepted: 10/11/2011] [Indexed: 11/17/2022]
Abstract
Vesicle transport requires four steps: vesicle formation, movement, tethering, and fusion. In yeast, two Rab GTPases, Ypt31/32, are required for post-Golgi vesicle formation. A third Rab GTPase, Sec4, and the exocyst act in tethering and fusion of these vesicles. Vesicle production is coupled to transport via direct interaction between Ypt31/32 and the yeast myosin V, Myo2. Here we show that Myo2 interacts directly with Sec4 and the exocyst subunit Sec15. Disruption of these interactions results in compromised growth and the accumulation of secretory vesicles. We identified the Sec15-binding region on Myo2 and also identified residues on Sec15 required for interaction with Myo2. That Myo2 interacts with Sec15 uncovers additional roles for the exocyst as an adaptor for molecular motors and implies similar roles for structurally related tethering complexes. Moreover, these studies predict that for many pathways, molecular motors attach to vesicles prior to their formation and remain attached until fusion.
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Affiliation(s)
- Yui Jin
- Life Sciences Institute, Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA
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Wani GM, Ahmad SM, Qayoom S, Khursheed B, Khan AR. Corticosteroid Induced, HHV-8 Positive Kaposi's Sarcoma in a Non-HIV Elderly Patient. J IMA 2012; 44:jima-44-1-09317. [PMID: 23864989 PMCID: PMC3708632 DOI: 10.5915/44-1-9317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Kaposi’s sarcoma (KS) was first described in 1872 by Moritz Kaposi. In 1994, Chang et al. first identified DNA sequences corresponding to human herpesvirus-8 (HHV-8) in AIDS-associated Kaposi sarcoma biopsies. It is now believed that presence of HHV-8 is necessary but not sufficient to cause KS. Other factors like immunosuppressive therapy also play a role. We describe an HIV-negative elderly patient who developed KS of skin and mucous membrane after prolonged use of corticosteroids for knee pain. The patient was positive for HHV-8.
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Affiliation(s)
- Gh Mohiuddin Wani
- Department of Dermatology, Venereology and Leprosy Sheri-Kashmir Institute of Medical Sciences (SKIMS)
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Singh S, Khan AR, Gupta AK. Role of glutathione in cancer pathophysiology and therapeutic interventions. J Exp Ther Oncol 2012; 9:303-316. [PMID: 22545423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Glutathione (GSH) is an important intracellular antioxidant that instills several vital roles within a cell including maintenance of the redox state, drug detoxification, and cellular protection from damage by free radicals, peroxides and toxins. Molecular alterations in the components of the GSH system in various tumors can lead to increased survival and enhanced tumor drug resistance. Early identification of the importance of intracellular GSH to detoxification reactions has now led to investigating the potential importance that GSH chemistry has on signal transduction, molecular regulation of cellular physiology and regulation of apoptosis pathway. Several therapeutic agents that target this system have been developed and used experimentally and clinically in an attempt to improve cancer chemotherapy. This review highlights different roles played by GSH that finally regulate tumor growth and advances in the use of GSH-based drugs to specifically target this detoxifying system in cancer treatment as a means to increase therapeutic response and decrease chemotherapeutic drug resistance.
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Affiliation(s)
- Simendra Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Gautam Budha Nagar, India.
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Khan NR, Khan GM, Wahab A, Khan AR, Hussain A, Nawaz A, Akhlaq M. Formulation, and physical, in vitro and ex vivo evaluation of transdermal ibuprofen hydrogels containing turpentine oil as penetration enhancer. Pharmazie 2011; 66:849-852. [PMID: 22204130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The aim of the present study was to investigate the transdermal permeation enhancing capability of turpentine oil for ibuprofen from hydrogels. Ibuprofen 1% w/v hydrogels were developed with carboxypolymethylene with and without turpentine oil. Turpentine oil was incorporated in increasing concentrations, i.e. 0.5, 1, 1.5, 2, 2.5 and 3% of the total gel formulation, and its permeation enhancing effect was examined. Gels were examined physically for pH, viscosity, spreadability, extrudability, smoothness and appearance. To study the in vitro and ex vivo permeation potential of formulated gels, permeation studies were performed with a Franz diffusion cell using cellulose membrane and excised rabbit abdominal skin. Ibuprofen hydrogel with 3% turpentine oil showed a maximum flux of 10.87 mg/cm2/h across artificial skin and 17.26 mg/cm2/h across rabbit abdominal skin.
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Affiliation(s)
- N R Khan
- Department of Pharmaceutics, Faculty of Pharmacy, Gomal University, D. I. Khan (Khyber Pakhtoonkhwa), Pakistan.
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Oliveira T, Panjikar S, Carrigan JB, Hamza M, Sharkey MA, Engel PC, Khan AR. Crystal structure of NAD+-dependent Peptoniphilus asaccharolyticus glutamate dehydrogenase reveals determinants of cofactor specificity. J Struct Biol 2011; 177:543-52. [PMID: 22068154 DOI: 10.1016/j.jsb.2011.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 10/16/2022]
Abstract
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of l-glutamate to α-ketoglutarate using NAD(P) as a cofactor. The bacterial enzymes are hexamers and each polypeptide consists of an N-terminal substrate-binding (Domain I) followed by a C-terminal cofactor-binding segment (Domain II). The reaction takes place at the junction of the two domains, which move as rigid bodies and are presumed to narrow the cleft during catalysis. Distinct signature sequences in the nucleotide-binding domain have been linked to NAD(+) vs. NADP(+) specificity, but they are not unambiguous predictors of cofactor preferences. Here, we have determined the crystal structure of NAD(+)-specific Peptoniphilus asaccharolyticus glutamate dehydrogenase in the apo state. The poor quality of native crystals was resolved by derivatization with selenomethionine, and the structure was solved by single-wavelength anomalous diffraction methods. The structure reveals an open catalytic cleft in the absence of substrate and cofactor. Modeling of NAD(+) in Domain II suggests that a hydrophobic pocket and polar residues contribute to nucleotide specificity. Mutagenesis and isothermal titration calorimetry studies of a critical glutamate at the P7 position of the core fingerprint confirms its role in NAD(+) binding. Finally, the cofactor binding site is compared with bacterial and mammalian enzymes to understand how the amino acid sequences and three-dimensional structures may distinguish between NAD(+) vs. NADP(+) recognition.
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Affiliation(s)
- Tânia Oliveira
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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Fernandes H, Franklin E, Khan AR. Crystallization of an engineered RUN domain of Rab6-interacting protein 1/DENND5. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:556-60. [PMID: 21543860 PMCID: PMC3087639 DOI: 10.1107/s174430911100724x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 02/25/2011] [Indexed: 11/10/2022]
Abstract
Effectors of the Rab small GTPases are large multi-domain proteins which have proved difficult to express in soluble form in Escherichia coli. Generally, effectors are recruited to a distinct subcellular compartment by active (GTP-bound) Rabs, which are linked to membranes by one or two prenylated Cys residues at their C-termini. Following recruitment via their Rab-binding domain (RBD), effectors carry out various aspects of vesicle formation, transport, tethering and fusion through their other domains. Previously, successful purification of the RUN-PLAT tandem domains (residues 683-1061) of the 1263-residue Rab6-interacting protein 1 (R6IP1) required co-expression with Rab6, as attempts to solubly express the effector alone were unsuccessful. R6IP1 is also known as DENN domain-containing protein 5 (DENND5) and is expressed as two isoforms, R6IP1A/B (DENND5A/B), which differ by 24 amino acids at the N-terminus. Here, a deletion in R6IP1 was engineered to enable soluble expression and to improve the quality of the crystals grown in complex with Rab6. A large 23-residue loop linking two α-helices in the RUN1 domain was removed and replaced with a short linker. This loop resides on the opposite face to the Rab6-binding site and is not conserved in the RUN-domain family. In contrast to wild-type R6IP1-Rab6 crystals, which took several weeks to grow to full size, the engineered R6IP1 (RPdel)-Rab6 crystals could be grown in a matter of days.
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Affiliation(s)
- Humberto Fernandes
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Edward Franklin
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
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Oliveira TF, Franklin E, Afonso JP, Khan AR, Oldham NJ, Pereira IAC, Archer M. Structural insights into dissimilatory sulfite reductases: structure of desulforubidin from desulfomicrobium norvegicum. Front Microbiol 2011; 2:71. [PMID: 21833321 PMCID: PMC3153041 DOI: 10.3389/fmicb.2011.00071] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [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: 02/09/2011] [Accepted: 03/28/2011] [Indexed: 11/29/2022] Open
Abstract
Dissimilatory sulfite reductases (dSiRs) are crucial enzymes in bacterial sulfur-based energy metabolism, which are likely to have been present in some of the earliest life forms on Earth. Several classes of dSiRs have been proposed on the basis of different biochemical and spectroscopic properties, but it is not clear whether this corresponds to actual physiological or structural differences. Here, we describe the first structure of a dSiR from the desulforubidin class isolated from Desulfomicrobium norvegicum. The desulforubidin (Drub) structure is assembled as α2β2γ2, in which two DsrC proteins are bound to the core [DsrA]2[DsrB]2 unit, as reported for the desulfoviridin (Dvir) structure from Desulfovibrio vulgaris. Unlike Dvir, four sirohemes and eight [4Fe–4S] clusters are present in Drub. However, the structure indicates that only two of the Drub coupled siroheme-[4Fe–4S] cofactors are catalytically active. Mass spectrometry studies of purified Drub and Dvir show that both proteins present different oligomeric complex forms that bind two, one, or no DsrC proteins, providing an explanation for conflicting spectroscopic and biochemical results in the literature, and further indicating that DsrC is not a subunit of dSiR, but rather a protein with which it interacts.
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Affiliation(s)
- Tânia F Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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McCannel CA, Khan AR. Spectral-domain optical coherence tomography assessment of an epiretinal membrane with axoplasmic stasis from nerve fiber layer traction. Retin Cases Brief Rep 2011; 5:358-359. [PMID: 25390435 DOI: 10.1097/icb.0b013e3182051e1f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
PURPOSE To report a case of visible axoplasmic stasis on fundus examination correlating with spectral-domain optical coherence tomography findings of nerve fiber layer traction. METHODS Case report. RESULTS Spectral-domain optical coherence tomography images show nerve fiber layer traction and distortion at the sites where visible cotton wool spot-like changes were seen on examination. These visible changes are likely because of axoplasmic stasis from the severe traction on the nerve fiber layer. CONCLUSION Spectral-domain optical coherence tomography demonstrates that cotton wool spot-like changes may be caused by nerve fiber layer traction in some epiretinal membranes. This is of interest in understanding the pathophysiology of these changes.
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Affiliation(s)
- Colin A McCannel
- From the *Jules Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; and †Mayo Clinic College of Medicine, Department of Ophthalmology, Rochester, Minnesota
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Khan AR, Khamseen MAB, Al Aithan MA, Khan SA, Al Ibrahim I, Al Abdul Lateef ZN. Knowledge, attitude and practice of ministry of health primary health care physicians in the management of type 2 diabetes mellitus: A cross-sectional study in the Al Hasa District of Saudi Arabia, 2010. Niger J Clin Pract 2011; 14:52-9. [DOI: 10.4103/1119-3077.79241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nagle PS, Quinn SJ, Kelly JM, O'Donovan DH, Khan AR, Rodriguez F, Nguyen B, Wilson WD, Rozas I. Understanding the DNA binding of novel non-symmetrical guanidinium/2-aminoimidazolinium derivatives. Org Biomol Chem 2010; 8:5558-67. [PMID: 20949223 PMCID: PMC3860747 DOI: 10.1039/c0ob00428f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biophysical studies have been carried out on a family of asymmetric guanidinium-based diaromatic derivatives to assess their potential as DNA minor groove binding agents. To experimentally assess the binding of these compounds to DNA, solution phase biophysical studies have been performed. Thus, surface plasmon resonance, UV-visible spectroscopy and circular and linear dichroism have been utilized to evaluate binding constants, stoichiometry and mode of binding. In addition, the thermodynamics of the binding process have been determined by using isothermal titration calorimetry. These results show significant DNA binding affinity that correlates with the expected 1 : 1 binding ratio usually observed for minor groove binders. Moreover, a simple computational approach has been devised to assess the potential as DNA binders of this family of compounds.
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Affiliation(s)
- Padraic S. Nagle
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Susan J. Quinn
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
| | - John M. Kelly
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Daniel H. O'Donovan
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Fernando Rodriguez
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Binh Nguyen
- Department of Chemistry, Georgia State University, USA
| | | | - Isabel Rozas
- School of Chemistry, University of Dublin, Trinity College, Dublin 2, Ireland
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