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Pitman C, Santiago-McRae E, Lohia R, Bassi K, Joseph TT, Hansen MEB, Brannigan G. The blobulator: a webtool for identification and visual exploration of hydrophobic modularity in protein sequences. bioRxiv 2024:2024.01.15.575761. [PMID: 38293114 PMCID: PMC10827107 DOI: 10.1101/2024.01.15.575761] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Motivation Clusters of hydrophobic residues are known to promote structured protein stability and drive protein aggregation. Recent work has shown that identifying contiguous hydrophobic residue clusters (termed "blobs") has proven useful in both intrinsically disordered protein (IDP) simulation and human genome studies. However, a graphical interface was unavailable. Results Here, we present the blobulator: an interactive and intuitive web interface to detect intrinsic modularity in any protein sequence based on hydrophobicity. We demonstrate three use cases of the blobulator and show how identifying blobs with biologically relevant parameters provides useful information about a globular protein, two orthologous membrane proteins, and an IDP. Other potential applications are discussed, including: predicting protein segments with critical roles in tertiary interactions, providing a definition of local order and disorder with clear edges, and aiding in predicting protein features from sequence. Availability The blobulator GUI can be found at www.blobulator.branniganlab.org, and the source code with pip installable command line tool can be found on GitHub at www.GitHub.com/BranniganLab/blobulator.
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Affiliation(s)
- Connor Pitman
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Ruchi Lohia
- Department of Physiology, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, Ontario, Canada
| | - Kaitlin Bassi
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, JMB 305, 3620 Hamilton Walk, 19104, PA, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, 19104, PA, USA
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
- Department of Physics, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA
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2
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Joseph TT, Bu W, Haji-Ghassemi O, Chen YS, Woll K, Allen PD, Brannigan G, van Petegem F, Eckenhoff RG. Propofol directly binds and inhibits skeletal muscle ryanodine receptor 1 (RyR1). bioRxiv 2024:2024.01.10.575040. [PMID: 38260485 PMCID: PMC10802444 DOI: 10.1101/2024.01.10.575040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
As the primary Ca 2+ release channel in skeletal muscle sarcoplasmic reticulum (SR), mutations in the type 1 ryanodine receptor (RyR1) or its binding partners underlie a constellation of muscle disorders, including malignant hyperthermia (MH). In patients with MH mutations, exposure to triggering drugs such as the halogenated volatile anesthetics biases RyR1 to an open state, resulting in uncontrolled Ca 2+ release, sarcomere tension and heat production. Restoration of Ca 2+ into the SR also consumes ATP, generating a further untenable metabolic load. When anesthetizing patients with known MH mutations, the non-triggering intravenous general anesthetic propofol is commonly substituted for triggering anesthetics. Evidence of direct binding of anesthetic agents to RyR1 or its binding partners is scant, and the atomic-level interactions of propofol with RyR1 are entirely unknown. Here, we show that propofol decreases RyR1 opening in heavy SR vesicles and planar lipid bilayers, and that it inhibits activator-induced Ca 2+ release from SR in human skeletal muscle. In addition to confirming direct binding, photoaffinity labeling using m- azipropofol (AziP m ) revealed several putative propofol binding sites on RyR1. Prediction of binding affinity by molecular dynamics simulation suggests that propofol binds at least one of these sites at clinical concentrations. These findings invite the hypothesis that in addition to propofol not triggering MH, it may also be protective against MH by inhibiting induced Ca 2+ flux through RyR1.
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Becker-Baldus J, Yeliseev A, Joseph TT, Sigurdsson ST, Zoubak L, Hines K, Iyer MR, van den Berg A, Stepnowski S, Zmuda J, Gawrisch K, Glaubitz C. Probing the Conformational Space of the Cannabinoid Receptor 2 and a Systematic Investigation of DNP-Enhanced MAS NMR Spectroscopy of Proteins in Detergent Micelles. ACS Omega 2023; 8:32963-32976. [PMID: 37720784 PMCID: PMC10500644 DOI: 10.1021/acsomega.3c04681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023]
Abstract
Tremendous progress has been made in determining the structures of G-protein coupled receptors (GPCR) and their complexes in recent years. However, understanding activation and signaling in GPCRs is still challenging due to the role of protein dynamics in these processes. Here, we show how dynamic nuclear polarization (DNP)-enhanced magic angle spinning nuclear magnetic resonance in combination with a unique pair labeling approach can be used to study the conformational ensemble at specific sites of the cannabinoid receptor 2. To improve the signal-to-noise, we carefully optimized the DNP sample conditions and utilized the recently introduced AsymPol-POK as a polarizing agent. We could show qualitatively that the conformational space available to the protein backbone is different in different parts of the receptor and that a site in TM7 is sensitive to the nature of the ligand, whereas a site in ICL3 always showed large conformational freedom.
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Affiliation(s)
- Johanna Becker-Baldus
- Institute
of Biophysical Chemistry and Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Alexei Yeliseev
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Thomas T. Joseph
- Department
of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Snorri Th. Sigurdsson
- Department
of Chemistry, Science Institute, University
of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | - Lioudmila Zoubak
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Kirk Hines
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Malliga R. Iyer
- Section
on Medicinal Chemistry, National Institute
on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Arjen van den Berg
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Sam Stepnowski
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Jon Zmuda
- ThermoFisher
Scientific, 7335 Executive
Way, Frederick, Maryland 21704, United States
| | - Klaus Gawrisch
- National
Institute on Alcohol Abuse and Alcoholism, National Institutes of
Health, Bethesda, Maryland 20852, United States
| | - Clemens Glaubitz
- Institute
of Biophysical Chemistry and Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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Santiago-McRae E, Petroff JT, Cheng WW, Joseph TT, Hénin J, Brannigan G. Absolute binding affinities of phospholipids to Erwinia ligand-gated ion channel (ELIC) by streamlined alchemical free energy perturbations (SAFEP). Biophys J 2023; 122:134a. [PMID: 36782605 DOI: 10.1016/j.bpj.2022.11.887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University Camden, Camden, NJ, USA
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Wayland W Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, Paris, France
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University Camden, Camden, NJ, USA; Department of Physics, Rutgers University Camden, Camden, NJ, USA
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Joseph TT, Bu W, Lin W, Zoubak L, Yeliseev A, Liu R, Eckenhoff RG, Brannigan G. Ketamine Metabolite (2 R,6 R)-Hydroxynorketamine Interacts with μ and κ Opioid Receptors. ACS Chem Neurosci 2021; 12:1487-1497. [PMID: 33905229 PMCID: PMC8154314 DOI: 10.1021/acschemneuro.0c00741] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
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Ketamine is an anesthetic,
analgesic, and antidepressant whose
secondary metabolite (2R,6R)-hydroxynorketamine
(HNK) has N-methyl-d-aspartate-receptor-independent
antidepressant activity in a rodent model. In humans, naltrexone attenuates
its antidepressant effect, consistent with opioid pathway involvement.
No detailed biophysical description is available of opioid receptor
binding of ketamine or its metabolites. Using molecular dynamics simulations
with free energy perturbation, we characterize the binding site and
affinities of ketamine and metabolites in μ and κ opioid
receptors, finding a profound effect of the protonation state. G-protein
recruitment assays show that HNK is an inverse agonist, attenuated
by naltrexone, in these receptors with IC50 values congruous
with our simulations. Overall, our findings are consistent with opioid
pathway involvement in ketamine function.
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Affiliation(s)
- Thomas T. Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Weiming Bu
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wenzhen Lin
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Lioudmila Zoubak
- National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Alexei Yeliseev
- National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Renyu Liu
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Roderic G. Eckenhoff
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University, Camden, New Jersey 08102, United States
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Wague A, Joseph TT, Woll KA, Bu W, Vaidya KA, Bhanu NV, Garcia BA, Nimigean CM, Eckenhoff RG, Riegelhaupt PM. Mechanistic insights into volatile anesthetic modulation of K2P channels. eLife 2020; 9:59839. [PMID: 33345771 PMCID: PMC7781597 DOI: 10.7554/elife.59839] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/19/2020] [Indexed: 01/01/2023] Open
Abstract
K2P potassium channels are known to be modulated by volatile anesthetic (VA) drugs and play important roles in clinically relevant effects that accompany general anesthesia. Here, we utilize a photoaffinity analog of the VA isoflurane to identify a VA-binding site in the TREK1 K2P channel. The functional importance of the identified site was validated by mutagenesis and biochemical modification. Molecular dynamics simulations of TREK1 in the presence of VA found multiple neighboring residues on TREK1 TM2, TM3, and TM4 that contribute to anesthetic binding. The identified VA-binding region contains residues that play roles in the mechanisms by which heat, mechanical stretch, and pharmacological modulators alter TREK1 channel activity and overlaps with positions found to modulate TASK K2P channel VA sensitivity. Our findings define molecular contacts that mediate VA binding to TREK1 channels and suggest a mechanistic basis to explain how K2P channels are modulated by VAs.
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Affiliation(s)
- Aboubacar Wague
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Kellie A Woll
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Weiming Bu
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Kiran A Vaidya
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
| | - Natarajan V Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, United States.,Department of Biochemistry, Weill Cornell Medical College, New York City, United States
| | - Roderic G Eckenhoff
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, United States
| | - Paul M Riegelhaupt
- Department of Anesthesiology, Weill Cornell Medical College, New York City, United States
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7
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Joseph TT, Wax DB, Goldstein R, Huang J, McCormick PJ, Levin MA. A Web-Based Perioperative Dashboard as a Platform for Anesthesia Informatics Innovation. Anesth Analg 2020; 131:1640-1645. [PMID: 33079890 PMCID: PMC8278241 DOI: 10.1213/ane.0000000000005193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Thomas T. Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania (Philadelphia, PA, USA)
| | - David B. Wax
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai (New York, NY, USA)
| | - Raymond Goldstein
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai (New York, NY, USA)
| | - Jia Huang
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai (New York, NY, USA)
| | - Patrick J. McCormick
- Department of Anesthesiology and Critical Care Medicine, Memorial Sloan-Kettering Cancer Center, (New York, NY, USA)
| | - Matthew A. Levin
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai (New York, NY, USA)
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Murlidaran S, Bu W, Eckenhoff RG, Brannigan GH, Joseph TT. Relative Affinities of General Anesthetics for Experimentally Identified Binding Sites in Ryanodine Receptors (RyR1). Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.771] [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: 12/01/2022] Open
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9
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McKinstry-Wu AR, Woll KA, Joseph TT, Bu W, White ER, Bhanu NV, Garcia BA, Brannigan G, Dailey WP, Eckenhoff RG. Azi-medetomidine: Synthesis and Characterization of a Novel α2 Adrenergic Photoaffinity Ligand. ACS Chem Neurosci 2019; 10:4716-4728. [PMID: 31638765 DOI: 10.1021/acschemneuro.9b00484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Agonists at the α2 adrenergic receptor produce sedation, increase focus, provide analgesia, and induce centrally mediated hypotension and bradycardia, yet neither their dynamic interactions with adrenergic receptors nor their modulation of neuronal circuit activity is completely understood. Photoaffinity ligands of α2 adrenergic agonists have the potential both to capture discrete moments of ligand-receptor interactions and to prolong naturalistic drug effects in discrete regions of tissue in vivo. We present here the synthesis and characterization of a novel α2 adrenergic agonist photolabel based on the imidazole medetomidine called azi-medetomidine. Azi-medetomidine shares protein association characteristics with its parent compound in experimental model systems and by molecular dynamics simulation of interactions with the α2A adrenergic receptor. Azi-medetomidine acts as an agonist at α2A adrenergic receptors, and produces hypnosis in Xenopus laevis tadpoles. Azi-medetomidine competes with the α2 agonist clonidine at α2A adrenergic receptors, which is potentiated by photolabeling, and azi-medetomidine labels moieties on the α2A adrenergic receptor as determined by mass spectrometry in a manner consistent with a simulated model. This novel α2 adrenergic agonist photolabel can serve as a powerful tool for in vitro and in vivo investigations of adrenergic signaling.
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Affiliation(s)
- Andrew R. McKinstry-Wu
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Kellie A. Woll
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Thomas T. Joseph
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Weiming Bu
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - E. Railey White
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Natarajan V. Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Department of Physics, Rutgers University, Camden, New Jersey 08102, United States
| | - William P. Dailey
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Roderic G. Eckenhoff
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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Wax DB, McCormick PJ, Joseph TT, Levin MA. An Automated Critical Event Screening and Notification System to Facilitate Preanesthesia Record Review. Anesth Analg 2018; 126:606-610. [PMID: 29053113 DOI: 10.1213/ane.0000000000002141] [Citation(s) in RCA: 8] [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] [Indexed: 11/05/2022]
Abstract
BACKGROUND Anesthesia information management systems make prior anesthesia records readily available for review when patients return for a subsequent procedure but may create a problem of too much documentation to review in a limited amount of time. We implemented a screening tool to facilitate the identification of critical documentation for review. METHODS An algorithm was developed to electronically search prior anesthesia records for predefined critical events and flag records containing these events. Our web-based daily case schedule was modified to contain a warning message for any patient on the schedule who has a prior record flagged by the system, in addition to a preexisting hyperlink to view the relevant record. A retrospective analysis was performed to determine the impact of the warning messages on the frequency with which the care team reviewed these records before providing anesthesia care. RESULTS The screening algorithm flagged 13% of archived cases as critical. There were 3329 and 3369 cases in the 6 months before and after system implementation, respectively, that had prior critical records available for review at that time. One or more of these critical records were viewed before the subsequent case start in 39% vs 59% (P < .01) of cases in the pre- versus postimplementation periods. Subgroup analysis revealed that the increase was greatest for attending anesthesiologists working alone. CONCLUSIONS We created a system to automatically detect critical events in prior anesthesia records for the purpose of forewarning the anesthesia care team when the same patient returns for another procedure. Inclusion of these warnings on the daily case schedule was associated with an increased frequency of preanesthesia review of old records.
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Affiliation(s)
- David B Wax
- From the Department of Anesthesiology, Perioperative, and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Patrick J McCormick
- Department of Anesthesiology and Critical Care, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Matthew A Levin
- From the Department of Anesthesiology, Perioperative, and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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Joseph TT, DiMeglio M, Huffenberger A, Laudanski K. Behavioural patterns of electrolyte repletion in intensive care units: lessons from a large electronic dataset. Sci Rep 2018; 8:11915. [PMID: 30093668 PMCID: PMC6085366 DOI: 10.1038/s41598-018-30444-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/26/2018] [Indexed: 11/29/2022] Open
Abstract
Repletion of electrolytes often depends on provider-specific behavior and hospital policy. We examined the pattern of electrolyte repletion across several intensive care units (ICU) in a large healthcare system from 2010–2015. This included 109 723 potassium repletions, 51 833 magnesium repletions, 2 306 calcium repletions, 8 770 phosphate repletions, and 3 128 249 visit-days over 332 018 visits. Potassium, magnesium, and calcium were usually repleted within the institutional reference range. In contrast, the bulk of phosphate repletion was done with pre-repletion serum level below the reference range. The impact of repletion on post-repletion levels was significant but uniformly small. The pre-repletion serum level had a significant inverse correlation with the post-repletion level of each electrolyte. Potassium, magnesium and phosphate follow-up labs were scheduled in 9–10 hours after their repletion. In contrast, calcium was rechecked in less than 20 minutes. Routine repletion of potassium, magnesium and calcium had no effect on the incidence of tachyarrhythmias. We estimated the expense from electrolyte repletion within the reference range was approximately $1.25 million. Absent a specific clinical indication, repleting electrolytes when the serum concentration are within normative values may represent an avenue for cost savings, staff burden unload and potential reduction in frequency of complications in the ICUs.
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Affiliation(s)
- Thomas T Joseph
- Department of Anaesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Matthew DiMeglio
- Center for Connected Medicine, University of Pennsylvania Health system, Philadelphia, USA
| | | | - Krzysztof Laudanski
- Department of Anaesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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12
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Joseph TT, Eckenhoff RG, Brannigan G. The pH Dependence of Ketamine Binding to G-Protein Coupled Receptors. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1260] [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: 11/16/2022] Open
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13
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Riegelhaupt PM, Woll KA, Joseph TT, Vaidya KA, Nimigean CM, Eckenhoff RG. Identification of a Modulatory Site of Action for the Volatile Anesthetic Isoflurane in TREK1 Tandem Pore Potassium Channels. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2675] [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: 10/18/2022] Open
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14
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Levin MA, Joseph TT, Jeff JM, Nadukuru R, Ellis SB, Bottinger EP, Kenny EE. iGAS: A framework for using electronic intraoperative medical records for genomic discovery. J Biomed Inform 2017; 67:80-89. [PMID: 28193464 DOI: 10.1016/j.jbi.2017.02.005] [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] [Received: 09/16/2016] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Design and implement a HIPAA and Integrating the Healthcare Enterprise (IHE) profile compliant automated pipeline, the integrated Genomics Anesthesia System (iGAS), linking genomic data from the Mount Sinai Health System (MSHS) BioMe biobank to electronic anesthesia records, including physiological data collected during the perioperative period. The resulting repository of multi-dimensional data can be used for precision medicine analysis of physiological readouts, acute medical conditions, and adverse events that can occur during surgery. MATERIALS AND METHODS A structured pipeline was developed atop our existing anesthesia data warehouse using open-source tools. The pipeline is automated using scheduled tasks. The pipeline runs weekly, and finds and identifies all new and existing anesthetic records for BioMe participants. RESULTS The pipeline went live in June 2015 with 49.2% (n=15,673) of BioMe participants linked to 40,947 anesthetics. The pipeline runs weekly in minimal time. After eighteen months, an additional 3671 participants were enrolled in BioMe and the number of matched anesthetic records grew 21% to 49,545. Overall percentage of BioMe patients with anesthetics remained similar at 51.1% (n=18,128). Seven patients opted out during this time. The median number of anesthetics per participant was 2 (range 1-144). Collectively, there were over 35 million physiologic data points and 480,000 medication administrations linked to genomic data. To date, two projects are using the pipeline at MSHS. CONCLUSION Automated integration of biobank and anesthetic data sources is feasible and practical. This integration enables large-scale genomic analyses that might inform variable physiological response to anesthetic and surgical stress, and examine genetic factors underlying adverse outcomes during and after surgery.
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Affiliation(s)
- Matthew A Levin
- Department of Anesthesiology, Division of Cardiothoracic Anesthesia, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA, USA
| | - Janina M Jeff
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Stephen B Ellis
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Eimear E Kenny
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA; The Icahn Institute of Multiscale Biology and Genomics, Icahn School of Medicine at Mount Sinai, New York, USA; The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, USA.
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15
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Tabrizian P, Joseph TT, Radkani P, Cohen E, Facciuto M. Liver Transplantation in an Adult Recipient With Situs Inversus Totalis: Case Report and Review of the Literature. Transplant Proc 2016; 48:3163-3166. [PMID: 27932172 DOI: 10.1016/j.transproceed.2016.06.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/12/2016] [Accepted: 06/06/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Over the past few decades, reports have demonstrated the feasibility of liver transplantation in adult patients with situs inversus. However, this disease entity remains rare and experience remains limited in adult recipients with situs inversus undergoing transplantation. METHODS A 23-year-old woman with situs inversus totalis and end-stage liver disease secondary to congenital biliary atresia was referred to our center and underwent a successful orthotopic liver transplantation. RESULTS We report our experience and review the literature. We performed a modified piggy-back technique with cavo-cavostomy. Using a triangulated wide orifice, the suprahepatic cava was anastomosed in an end-to-side fashion. The patient underwent an uneventful hospitalization and recovery. CONCLUSION Situs inversus remains a rare condition. Careful perioperative planning, thorough anatomic knowledge of both donor and recipient liver, and use of a variety of different novel techniques can lead to successful outcomes.
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Affiliation(s)
- P Tabrizian
- Department of Transplantation, Recanati/Miller Transplantation Institute, Mount Sinai Medical Center, New York, New York, USA
| | - T T Joseph
- Department of Anesthesiology, Mount Sinai Medical Center, New York, New York, USA
| | - P Radkani
- Department of Transplantation, Recanati/Miller Transplantation Institute, Mount Sinai Medical Center, New York, New York, USA
| | - E Cohen
- Department of Anesthesiology, Mount Sinai Medical Center, New York, New York, USA
| | - M Facciuto
- Department of Transplantation, Recanati/Miller Transplantation Institute, Mount Sinai Medical Center, New York, New York, USA.
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16
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Joseph TT, Osman R. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network. PLoS Comput Biol 2012; 8:e1002693. [PMID: 23028290 PMCID: PMC3459882 DOI: 10.1371/journal.pcbi.1002693] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 03/21/2012] [Accepted: 07/28/2012] [Indexed: 11/19/2022] Open
Abstract
In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the cumulative effects of a large number of internal allosteric pathways.
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Affiliation(s)
- Thomas T. Joseph
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- Computational Biology Program, New York University, New York, New York, United States of America
| | - Roman Osman
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- Computational Biology Program, New York University, New York, New York, United States of America
- * E-mail:
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Joseph TT, Osman R. Thermodynamic basis of selectivity in guide-target-mismatched RNA interference. Proteins 2012; 80:1283-98. [PMID: 22275138 DOI: 10.1002/prot.24025] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/08/2011] [Accepted: 12/21/2011] [Indexed: 01/21/2023]
Abstract
Silencing in RNAi is strongly affected by guide-strand/target-mRNA mismatches. Target nucleation is thought to occur at positions 2-8 of the guide ("seed region"); successful hybridization in this region is the primary determinant of target-binding affinity and hence target cleavage. To define a molecular basis for the target sequence selectivity in RNAi, we studied all possible distinct single mismatches in seven positions of the seed region-a total of 21 substitutions. We report results from soft-core thermodynamic integration simulations to determine changes in targeting binding-free energies to Argonaute due to single mismatches in the guide strand, which arise during binding of an imperfectly matched target mRNA. In agreement with experiment, most mismatches impair target binding, consistent with a prominent role for binding affinity changes in RNAi sequence selectivity. Individual Argonaute residues located near the mismatched base pair are found to contribute significantly to binding affinity changes. We also use this methodology to analyze the mismatch-dependent free energy changes for dissociation of a DNA•RNA hybrid from Argonaute, as a model for the escape of miRNAs from the silencing pathway. Several mismatched sequences of the miRNA have increased affinity to Argonaute, implying that some mismatches may reduce the probability for escape. Furthermore, calculations of base-substitution-dependent free energy changes for binding ssDNA reveal mild sequence sensitivity as expected for guide strand binding to Argonaute. Our findings give a thermodynamic basis for RNAi target sequence selectivity and suggest that miRNA mismatches may increase silencing effectiveness and thus could be evolutionarily advantageous.
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Affiliation(s)
- Thomas T Joseph
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, New York, New York, USA
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