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Oteir AO, Jennings PA, Smith K, Stoelwinder J. Should suspected cervical spinal cord injuries be immobilised? A systematic review protocol. Inj Prev 2013; 20:e5. [PMID: 24324194 DOI: 10.1136/injuryprev-2013-041080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Cervical spinal cord injuries may result in life-threatening situations and long-term disability. Prehospital spinal immobilisation is the standard of care for patients with potential spinal cord injury (SCI). It aims to prepare patients for transport, achieve neutral spinal alignment, and reduce movement and secondary injuries in potentially unstable spines. However, there is a lack of evidence on its clinical benefits and its overall effect on patient outcomes. OBJECTIVES To identify the reported outcomes following immobilisation of suspected cervical SCI, to compare the effects of spinal immobilisation versus no immobilisation on the reported outcomes, and to provide recommendations for prehospital cervical immobilisation. DESIGN/METHODS A search of the literature will be conducted using relevant online databases. This will include all types of human studies that were published in English from the earliest record available to the first week of October 2013. One author will conduct the search and two independent authors will screen the titles and the abstracts identified by the search and critically appraise the selected papers. A third author will be available to resolve any disagreement. The findings will be reported according to Preferred Reporting Items for Systematic Reviews (PRISMA) guidelines. Critical appraisal as well as the level and the strength of evidence will follow the National Health and Medical Research Council (NHMRC) guidelines. DISCUSSION Evidence-based practices should be pursued to further improve the prehospital care for suspected cervical SCI. This systematic review will contribute to the body of knowledge regarding the spinal immobilisation effects on the SCI patient's outcomes.
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Williams B, Jennings PA, Fielder C, Ghirardello A. Next generation paramedics, agents of change, or time for curricula renewal? ADVANCES IN MEDICAL EDUCATION AND PRACTICE 2013; 4:245-250. [PMID: 24244101 PMCID: PMC3828015 DOI: 10.2147/amep.s53085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND Knowledge translation involves the dissemination and application of scientific research findings into clinical practice. In the health care arena, uptake of evidence-based assessment and intervention strategies is aimed at reducing inefficiencies and ultimately improving patient outcomes. However, numerous studies have purported gaps in knowledge translation in the health care professions. The objective of this study was to classify the traits of undergraduate paramedic students from Monash Univeristy, Australia, using the practice style inventory (PSI). METHODS A cross-sectional study of students across all undergraduate years from Emergency Health and Emergency Health/Nursing was completed. Student knowledge translation levels were measured using the 17-item paper-based PSI. RESULTS A total of 266 students participated in the study, of which 68.4% were females. The majority of participants were <26 years of age (n=228) and just over half enrolled in second year studies (n=134). Two subscales produced statistically significant differences: evidence versus experience (extent to which scientific evidence rather than authority is perceived as the best source of knowledge) and nonconformity (degree of comfort with clinical practices that are out of step with recommendations of leaders). There was a statistically significant difference between sex on the evidence versus experience subscale (P<0.0001, d =0.51), and between year levels on the nonconformity subscale (P<0.007, d =0.63). CONCLUSION This study identified several differences in knowledge translation subscales in the undergraduate paramedic cohorts. Further investigation is warranted in order to better understand barriers and facilitate improved uptake of evidence-based research into clinical practice and, ultimately, improve patient outcomes. Future research using a longitudinal study design to capture changing attitudes to knowledge translation in the postgraduate population may also prove valuable in curricula renewal.
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Mackrill JB, Jennings PA, Cain R. Improving the hospital 'soundscape': a framework to measure individual perceptual response to hospital sounds. ERGONOMICS 2013; 56:1687-1697. [PMID: 24073684 DOI: 10.1080/00140139.2013.835873] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Work on the perception of urban soundscapes has generated a number of perceptual models which are proposed as tools to test and evaluate soundscape interventions. However, despite the excessive sound levels and noise within hospital environments, perceptual models have not been developed for these spaces. To address this, a two-stage approach was developed by the authors to create such a model. First, semantics were obtained from listening evaluations which captured the feelings of individuals from hearing hospital sounds. Then, 30 participants rated a range of sound clips representative of a ward soundscape based on these semantics. Principal component analysis extracted a two-dimensional space representing an emotional-cognitive response. The framework enables soundscape interventions to be tested which may improve the perception of these hospital environments.
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Jennings PA, Cameron P, Bernard S, Walker T, Jolley D, Fitzgerald M, Masci K. Long-term pain prevalence and health-related quality of life outcomes for patients enrolled in a ketamine versus morphine for prehospital traumatic pain randomised controlled trial. Emerg Med J 2013; 31:840-3. [DOI: 10.1136/emermed-2013-202862] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Schricke DI, Jennings PA, Edgar DW, Harvey JG, Cleland HJ, Wood FM, Cameron PA. WITHDRAWN: Scald burns in children aged 14 and younger in Australia and New Zealand-An analysis based on the Bi-National Burns Registry (BiNBR). Burns 2013:S0305-4179(13)00157-5. [PMID: 23790638 DOI: 10.1016/j.burns.2013.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/20/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Abstract
Kinetic data measured from folding of the protein interleukin-1β fits best to three exponential phases when studied with tryptophan fluorescence but only two exponential phases when measured using other methods. The technique of ANS fluorescence was used to determine whether the additional phase observed in tryptophan fluorescence was also detected with ANS dye binding. Unlike trytophan fluorescence, the ANS fluorescence was highly dependent on the concentration of protein present during the folding experiment. Experimental controls provide evidence that ANS binds to protein aggregates, present at higher concentrations and absent at lower concentrations. Protein concentration-dependent folding studies demonstrate that, at lower interleukin-1β concentrations, tryptophan fluorescence kinetics can be fit adequately with a two exponential fit. This study indicates that (1) measured interleukin-1β folding kinetics fit to a 2 phase model and (2) at higher protein concentrations, transient association of IL-1β may result in a kinetic fit of 3 phases.
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Bayley PJ, Isaac L, Kong JY, Adamson MM, Ashford JW, Mahoney LA, Beltran M, Brown-Elhillali A, Held A, Ajayi A, Belcher H, Bond A, Mason H, Lemaster C, Shaw S, Mullin C, Holick E, Saper R, Braun TD, Riley KE, Park CL, Trehern AE, Davis MB, Mastronardi EL, Butzer B, Khalsa SBS, Shorter SM, Reinhardt KM, Cope S, Cheung C, Justice C, Wyman J, Cook-Cottone CP, Daly LA, Haden SC, Hagins M, Danhauer SC, Griffin LP, Avis NE, Sohl SJ, Lawrence J, Jesse MT, Addington EL, Messino MJ, Giguere JK, Lucas SL, Wiliford SK, Shaw E, de Manincor M, Bensoussan A, Smith C, Fahey P, Bourchier S, Desrochers DIM, Viswanathan S, Partharasathy BR, Doherty K, Moye J, Walsh C, Pokaski-Azar J, Gosian J, Chapman J, King K, Sohl S, Danhauer S, Dunbar E, Gabriel MG, Huebner M, Hofmann SG, Khalsa SBS, Gaskins RB, Jennings E, Thind H, Fava JL, Hartman S, Bock BC, Gramann P, Haaz S, Bingham CO, Bartlett SJ, Hagins M, States R, Selfe T, Innes K, Harris AR, Jennings PA, Abenavoli RM, Katz DA, Hudecek KM, Greenberg MT, Jeter PE, Nkodo AF, Haaz S, Dagnelie G, Keosaian JE, Lemaster CM, Chao M, Saper RB, King KD, Gosian J, Doherty K, Walsh C, Pokaski Azar J, Chapman J, Danhauer SC, Moye J, Kinser P, Bourguignon C, Taylor A, Mahoney LA, Bayley PJ, Collery LM, Menzies-Toman D, Nilsson M, Frykman V, Noggle JJ, Braun T, Khalsa SBS, Nosaka M, Okamura H, Fukatu N, Potts A, Weidknecht K, Coulombe S, Davies B, Ryan C, Day D, Reale J, Staples JK, Knoefel J, Herman C, Riley KE, Park CL, Bedesin EY, Stewart VM, Riley KE, Braun TD, Park CL, Pescatello LS, Davis MB, Trehern AE, Mastronardi EL, Rioux J, Rosen RK, Thind H, Gaskins R, Jennings E, Morrow K, Williams D, Bock B, Rousseau D, Jackson E, Schmid AA, Miller KK, Van Puymbroeck M, Debaun EL, Schalk N, Dierks TD, Altenburger P, Damush T, Williams LS, Selman L, Citron T, Howie-Esquivel J, McDermott K, Milic M, Donesky D, Shook A, Ruzic R, Galloway F, Van Puymbroeck M, Miller KK, Schalk N, Schmid AA, Ward LJ, Stebbings S, Sherman K, Cherkin D, Baxter GD, West JI, Duffy N, Liang B. 2013 SYR Accepted Poster Abstracts. Int J Yoga Therap 2013; 23:32-53. [PMID: 24016822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Jennings PA, Harriss L, Bernard S, Bray J, Walker T, Spelman T, Smith K, Cameron P. An automated CPR device compared with standard chest compressions for out-of-hospital resuscitation. BMC Emerg Med 2012; 12:8. [PMID: 22734854 PMCID: PMC3441844 DOI: 10.1186/1471-227x-12-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 06/21/2012] [Indexed: 11/22/2022] Open
Abstract
Background Effective cardiopulmonary resuscitation and increased coronary perfusion pressures have been linked to improved survival from cardiac arrest. This study aimed to compare the rates of survival between conventional cardiopulmonary resuscitation (C-CPR) and automated CPR (A-CPR) using AutoPulse™ in adults following out-of-hospital cardiac arrest (OHCA). Methods This was a retrospective study using a matched case–control design across three regional study sites in Victoria, Australia. Each case was matched to at least two (maximum four) controls using age, gender, response time, presenting cardiac rhythm and bystander CPR, and analysed using conditional fixed-effects logistic regression. Results During the period 1 October 2006 to 30 April 2010 there were 66 OHCA cases using A-CPR. These were matched to 220 cases of OHCA involving the administration of C-CPR only (controls). Survival to hospital was achieved in 26% (17/66) of cases receiving A-CPR compared with 20% (43/220) of controls receiving C-CPR and the propensity score adjusted odds ratio [AOR (95% CI)] was 1.69 (0.79, 3.63). Results were similar using only bystander witnessed OHCA cases with presumed cardiac aetiology. Survival to hospital was achieved for 29% (14/48) of cases receiving A-CPR compared with 18% (21/116) of those receiving C-CPR [AOR = 1.80 (0.78, 4.11)]. Conclusions The use of A-CPR resulted in a higher rate of survival to hospital compared with C-CPR, yet a tendency for a lower rate of survival to hospital discharge, however these associations did not reach statistical significance. Further research is warranted which is prospective in nature, involves randomisation and larger number of cases to investigate potential sub-group benefits of A-CPR including survival to hospital discharge.
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Jennings PA, Cameron P, Bernard S. Determinants of clinically important pain severity reduction in the prehospital setting. Emerg Med J 2011; 29:333-4. [PMID: 21252175 DOI: 10.1136/emj.2010.107094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This retrospective, electronic patient care record review examined a consecutive sample of patients presenting with pain to the metropolitan region of Ambulance Victoria over a 12 month period in 2008. Seven factors were found to be associated with the likelihood of clinically important pain reduction following multivariate analyses. These included age, time criticality of the patient, pain aetiology, initial pain severity, analgesic agent or combination administered to the patient and prehospital time.
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Morrison LJ, Deakin CD, Morley PT, Callaway CW, Kerber RE, Kronick SL, Lavonas EJ, Link MS, Neumar RW, Otto CW, Parr M, Shuster M, Sunde K, Peberdy MA, Tang W, Hoek TLV, Böttiger BW, Drajer S, Lim SH, Nolan JP, Adrie C, Alhelail M, Battu P, Behringer W, Berkow L, Bernstein RA, Bhayani SS, Bigham B, Boyd J, Brenner B, Bruder E, Brugger H, Cash IL, Castrén M, Cocchi M, Comadira G, Crewdson K, Czekajlo MS, Davies SR, Dhindsa H, Diercks D, Dine CJ, Dioszeghy C, Donnino M, Dunning J, El Sanadi N, Farley H, Fenici P, Feeser VR, Foster JA, Friberg H, Fries M, Garcia-Vega FJ, Geocadin RG, Georgiou M, Ghuman J, Givens M, Graham C, Greer DM, Halperin HR, Hanson A, Holzer M, Hunt EA, Ishikawa M, Ioannides M, Jeejeebhoy FM, Jennings PA, Kano H, Kern KB, Kette F, Kudenchuk PJ, Kupas D, La Torre G, Larabee TM, Leary M, Litell J, Little CM, Lobel D, Mader TJ, McCarthy JJ, McCrory MC, Menegazzi JJ, Meurer WJ, Middleton PM, Mottram AR, Navarese EP, Nguyen T, Ong M, Padkin A, Ferreira de Paiva E, Passman RS, Pellis T, Picard JJ, Prout R, Pytte M, Reid RD, Rittenberger J, Ross W, Rubertsson S, Rundgren M, Russo SG, Sakamoto T, Sandroni C, Sanna T, Sato T, Sattur S, Scapigliati A, Schilling R, Seppelt I, Severyn FA, Shepherd G, Shih RD, Skrifvars M, Soar J, Tada K, Tararan S, Torbey M, Weinstock J, Wenzel V, Wiese CH, Wu D, Zelop CM, Zideman D, Zimmerman JL. Part 8: Advanced Life Support. Circulation 2010; 122:S345-421. [DOI: 10.1161/circulationaha.110.971051] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jennings PA, Stella J. Barriers to incident notification in a regional prehospital setting. Emerg Med J 2010; 28:526-9. [PMID: 20581408 DOI: 10.1136/emj.2010.090738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND The identification and monitoring of critical incidents or adverse events and error reporting is a relatively new area of study in the prehospital setting. In 2005, we commenced a prospective descriptive study of the implementation of a Critical Incident Monitoring process in a rural/regional pre-hospital setting. The objective of the project was to describe the nature and incidence of errors detected in the management of prehospital trauma with the ultimate aim of identifying processes to reduce or mitigate such incidents. This paper describes the barriers to reporting critical incidents identified during the 3-year study. METHOD This study used a qualitative approach involving the triangulation of a number of ethnographic methodologies, including unscripted focus groups, informal interviews and qualitative aspects of surveys utilised in a broader research project. Prevailing themes were fed back to participants in an iterative process to further explore perceptions and beliefs regarding these concepts. The final analysis of themes is descriptively presented. RESULTS A number of barriers were identified and categorised into seven themes. These themes were; Burden of reporting, fear of disciplinary action, fear of potential litigation, fear of breaches of confidentiality and fear of embarrassment, concern that 'nothing would change' even if the incident was reported, lack of familiarity with process and impact of 'blame culture'. CONCLUSION There are numerous barriers to reporting critical incidents. One of the key approaches which may alleviate many of the barriers to reporting is shifting to a systems based focus rather than an individual 'shame and blame' approach. The underlying barriers lie in the culture of the profession, and appear consistent across other health care disciplines.
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Abstract
Severe pain is a common presenting symptom for emergency patients. One major challenge in the management of severe pain is the objective measurement of pain. Due to the subjective nature of pain, it can be very difficult for clinicians to quantify pain intensity and measure the qualitative features of the pain experience. A number of measurement tools have been validated in the acute care setting, with some appropriate for use in the prehospital setting. This paper reviews the characteristics required of a prehospital acute pain measure and appraises the relative utility of a number of currently used pain measures. At present, the verbal numerical rating scale appears the most appropriate pain measure to administer in the prehospital setting for adult patients as it is practical and valid. Either the Oucher scale or the faces pain scale is suitable for prehospital care providers to assess pain in children.
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Jennings PA, Cameron P, Walker T, Bernard S, Smith K. Out‐of‐hospital cardiac arrest in Victoria: rural and urban outcomes. Med J Aust 2006; 185:135-9. [PMID: 16893352 DOI: 10.5694/j.1326-5377.2006.tb00498.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 05/01/2006] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To compare the survival rate from out-of-hospital cardiac arrest in rural and urban areas of Victoria, and to investigate the factors associated with these differences. DESIGN Retrospective case series using data from the Victorian Ambulance Cardiac Arrest Registry. SETTING All out-of-hospital cardiac arrests occurring in Victoria that were attended by Rural Ambulance Victoria or the Metropolitan Ambulance Service. PARTICIPANTS 1790 people who suffered a bystander-witnessed cardiac arrest between January 2002 and December 2003. RESULTS Bystander cardiopulmonary resuscitation was more likely in rural (65.7%) than urban areas (48.4%) (P = 0.001). Urban patients with bystander-witnessed cardiac arrest were more likely to arrive at an emergency department with a cardiac output (odds ratio [OR], 2.92; 95% CI, 1.65-5.17; P < 0.001), and to be discharged from hospital alive than rural patients (urban, 125/1685 [7.4%]; rural, 2/105 [1.9%]; OR, 4.13; 95% CI, 1.09-34.91). Major factors associated with survival to hospital admission were distance of cardiac arrest from the closest ambulance branch (OR, 0.87; 95% CI, 0.82-0.92), endotracheal intubation (OR, 3.46; 95% CI, 2.49-4.80), and the presence of asystole (OR, 0.50; 95% CI, 0.38-0.67) or pulseless electrical activity (OR, 0.73; 95% CI, 0.56-0.95) on arrival of the first ambulance crew. CONCLUSIONS Survival rates differ between urban and rural cardiac arrest patients. This is largely due to a difference in ambulance response time. As it is impractical to substantially decrease response times in rural areas, other strategies that may improve outcome after cardiac arrest require investigation.
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Morikis D, Elcock AH, Jennings PA, McCammon JA. Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Sci 2001; 10:2379-92. [PMID: 11604543 PMCID: PMC2374072 DOI: 10.1110/ps.17301] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The enzyme glycinamide ribonucleotide transformylase (GART) catalyzes the transfer of a formyl group from formyl tetrahydrofolate (fTHF) to glycinamide ribonucleotide (GAR), a process that is pH-dependent with pK(a) of approximately 8. Experimental studies of pH-rate profiles of wild-type and site-directed mutants of GART have led to the proposal that His108, Asp144, and GAR are involved in catalysis, with His108 being an acid catalyst, while forming a salt bridge with Asp144, and GAR being a nucleophile to attack the formyl group of fTHF. This model implied a protonated histidine with pK(a) of 9.7 and a neutral GAR with pK(a) of 6.8. These proposed unusual pK(a)s have led us to investigate the electrostatic environment of the active site of GART. We have used Poisson-Boltzmann-based electrostatic methods to calculate the pK(a)s of all ionizable groups, using the crystallographic structure of a ternary complex of GART involving the pseudosubstrate 5-deaza-5,6,7,8-THF (5dTHF) and substrate GAR. Theoretical mutation and deletion analogs have been constructed to elucidate pairwise electrostatic interactions between key ionizable sites within the catalytic site. Also, a construct of a more realistic catalytic site including a reconstructed pseudocofactor with an attached formyl group, in an environment with optimal local van der Waals interactions (locally minimized) that imitates closely the catalytic reactants, has been used for pK(a) calculations. Strong electrostatic coupling among catalytic residues His108, Asp144, and substrate GAR was observed, which is extremely sensitive to the initial protonation and imidazole ring flip state of His108 and small structural changes. We show that a proton can be exchanged between GAR and His108, depending on their relative geometry and their distance to Asp144, and when the proton is attached on His108, catalysis could be possible. Using the formylated locally minimized construct of GART, a high pK(a) for His108 was calculated, indicating a protonated histidine, and a low pK(a) for GAR(NH(2)) was calculated, indicating that GAR is in neutral form. Our results are in qualitative agreement with the current mechanistic picture of the catalytic process of GART deduced from the experimental data, but they do not reproduce the absolute magnitude of the pK(a)s extracted from fits of k(cat)-pH profiles, possibly because the static time-averaged crystallographic structure does not describe adequately the dynamic nature of the catalytic site during binding and catalysis. In addition, a strong effect on the pK(a) of GAR(NH(2)) is produced by the theoretical mutations of His108Ala and Asp144Ala, which is not in agreement with the observed insensitivity of the pK(a) of GAR(NH(2)) modeled from the experimental data using similar mutations. Finally, we show that important three-way electrostatic interactions between highly conserved His137, with His108 and Asp144, are responsible for stabilizing the electrostatic microenvironment of the catalytic site. In conclusion, our data suggest that further detailed computational and experimental work is necessary.
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Morikis D, Elcock AH, Jennings PA, McCammon JA. Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. Protein Sci 2001; 10:2363-78. [PMID: 11604542 PMCID: PMC2374060 DOI: 10.1110/ps.17201] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Glycinamide ribonucleotide transformylase (GART) undergoes a pH-dependent coil-helix transition with pK(a) approximately 7. An alpha-helix is formed at high pH spanning 8 residues of a 21-residue-long loop, comprising the segment Thr120-His121-Arg122-Gln123-Ala124-Leu125-Glu126-Asn127. To understand the electrostatic nature of this loop-helix, called the activation loop-helix, which leads to the formation and stability of the alpha-helix, pK(a) values of all ionizable residues of GART have been calculated, using Poisson-Boltzmann electrostatic calculations and crystallographic data. Crystallographic structures of high and low pH E70A GART have been used in our analysis. Low pK(a) values of 5.3, 5.3, 3.9, 1.7, and 4.7 have been calculated for five functionally important histidines, His108, His119, His121, His132, and His137, respectively, using the high pH E70A GART structure. Ten theoretical single and double mutants of the high pH E70A structure have been constructed to identify pairwise interactions of ionizable residues, which have aided in elucidating the multiplicity of electrostatic interactions of the activation loop-helix, and the impact of the activation helix on the catalytic site. Based on our pK(a) calculations and structural data, we propose that: (1) His121 forms a molecular switch for the coil-helix transition of the activation helix, depending on its protonation state; (2) a strong electrostatic interaction between His132 and His121 is observed, which can be of stabilizing or destabilizing nature for the activation helix, depending on the relative orientation and protonation states of the rings of His121 and His132; (3) electrostatic interactions involving His119 and Arg122 play a role in the stability of the activation helix; and (4) the activation helix contains the helix-promoting sequence Arg122-Gln123-Ala124-Leu125-Glu126, but its alignment relative to the N and C termini of the helix is not optimal, and is possibly of a destabilizing nature. Finally, we provide electrostatic evidence that the formation and closure of the activation helix create a hydrophobic environment for catalytic-site residue His108, to facilitate catalysis.
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Dalrymple BP, Kongsuwan K, Wijffels G, Dixon NE, Jennings PA. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci U S A 2001; 98:11627-32. [PMID: 11573000 PMCID: PMC58780 DOI: 10.1073/pnas.191384398] [Citation(s) in RCA: 243] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction between DNA polymerases and sliding clamp proteins confers processivity in DNA synthesis. This interaction is critical for most DNA replication machines from viruses and prokaryotes to higher eukaryotes. The clamp proteins also participate in a variety of dynamic and competing protein-protein interactions. However, clamp-protein binding sequences have not so far been identified in the eubacteria. Here we show from three lines of evidence, bioinformatics, yeast two-hybrid analysis, and inhibition of protein-protein interaction by modified peptides, that variants of a pentapeptide motif (consensus QL[SD]LF) are sufficient to enable interaction of a number of proteins with an archetypal eubacterial sliding clamp (the beta subunit of Escherichia coli DNA polymerase III holoenzyme). Representatives of this motif are present in most sequenced members of the eubacterial DnaE, PolC, PolB, DinB, and UmuC families of DNA polymerases and the MutS1 mismatch repair protein family. The component tripeptide DLF inhibits the binding of the alpha (DnaE) subunit of E. coli DNA polymerase III to beta at microM concentration, identifying key residues. Comparison of the eubacterial, eukaryotic, and archaeal sliding clamp binding motifs suggests that the basic interactions have been conserved across the evolutionary landscape.
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Clementi C, Jennings PA, Onuchic JN. Prediction of folding mechanism for circular-permuted proteins. J Mol Biol 2001; 311:879-90. [PMID: 11518537 DOI: 10.1006/jmbi.2001.4871] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent theoretical and experimental studies have suggested that real proteins have sequences with sufficiently small energetic frustration that topological effects are central in determining the folding mechanism. A particularly interesting and challenging framework for exploring and testing the viability of these energetically unfrustrated models is the study of circular-permuted proteins. Here we present the results of the application of a topology-based model to the study of circular permuted SH3 and CI2, in comparison with the available experimental results. The folding mechanism of the permuted proteins emerging from our simulations is in very good agreement with the experimental observations. The differences between the folding mechanisms of the permuted and wild-type proteins seem then to be strongly related to the change in the native state topology.
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Andersen MD, Shaffer J, Jennings PA, Adams JA. Structural characterization of protein kinase A as a function of nucleotide binding. Hydrogen-deuterium exchange studies using matrix-assisted laser desorption ionization-time of flight mass spectrometry detection. J Biol Chem 2001; 276:14204-11. [PMID: 11278927 DOI: 10.1074/jbc.m011543200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient state kinetic studies indicate that substrate phosphorylation in protein kinase A is partially rate-limited by conformational changes, some of which may be associated with nucleotide binding (Shaffer, J., and Adams, J. A. (1999) Biochemistry 38, 12072-12079). To assess whether specific structural changes are associated with the binding of nucleotides, hydrogen-deuterium exchange experiments were performed on the enzyme in the absence and presence of ADP. Four regions of the protein are protected from exchange in the presence of ADP. Two regions encompass the catalytic and glycine-rich loops and are integral parts of the active site. Conversely, protection of probes in the C terminus is consistent with nucleotide-induced domain closure. One protected probe encompasses a portion of helix C, a secondary structural element that does not make any direct contacts with the nucleotide but has been reported to undergo segmental motion upon the activation of some protein kinases. The combined data suggest that binding of the nucleotide has distal structural effects that may include stabilizing the closed state of the enzyme and altering the position of a critical helix outside the active site. The latter represents the first evidence that the nucleotide alone can induce changes in helix C in solution.
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Covalt JC, Roy M, Jennings PA. Core and surface mutations affect folding kinetics, stability and cooperativity in IL-1 beta: does alteration in buried water play a role? J Mol Biol 2001; 307:657-69. [PMID: 11254388 DOI: 10.1006/jmbi.2001.4482] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Interleukin-1 beta (IL-1 beta) is a cytokine and a member of the beta-trefoil superfamily of protein structures. An interesting feature in the folding of IL-1 beta, shared with some other members of the same topological family, is the existence of a slow step in folding to the native conformation from a discrete intermediate. Wanting to probe the nature of this slow step in the folding of WT IL-1 beta (tau(1)=45 seconds), we made ten sequence variants of IL-1 beta (L10A, T9Q, T9G, C8S, C8A, N7G, N7D, L6A, R4P, and R4Q), where all mutations are located along strand 1. This strand is not protected from hydrogen exchange until late in folding. Most of the mutations showed little effect on the kinetics of folding for IL-1 beta. However, C8 is clearly involved in both the late and the early steps in folding, while sequence variants at L10 and L6 affect only late events in folding. The value of the slowest relaxation time, tau(1), which is associated with the rate of native protein formation, increased for the refolding of C8S, while C8A, L6A, and L10A showed smaller but systematic increases in the value of tau(1.)For both C8S and C8A, the value of the step associated with formation of the intermediate, tau(2), was independent of denaturant concentration. In addition, mutations in the hydrophobic core (L10A, C8A, C8S, and L6A) and, surprisingly, along the surface (T9G, T9Q, and N7G) alter the stability. The most destabilizing mutations show changes in equilibrium unfolding cooperativity, which is atypical for destabilizing mutations in IL-1 beta. Crystallographic studies indicate that mutations along strand 1 may alter the number of ordered water molecules within the core. Thus, side-chain replacement in this region can disrupt essential main-chain interactions mediated by ordered water contacts in a highly cooperative network of hydrogen bonding.
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Finke JM, Gross LA, Ho HM, Sept D, Zimm BH, Jennings PA. Commitment to folded and aggregated states occurs late in interleukin-1 beta folding. Biochemistry 2000; 39:15633-42. [PMID: 11112552 DOI: 10.1021/bi001307d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A point mutation, lysine 97 to isoleucine, in the all-beta cytokine interleukin-1 beta (IL-1 beta) exhibits an increased propensity to form inclusion bodies in vivo and aggregates in vitro. In an effort to better understand the aggregation reaction and determine when intervention may allow rescue of protein from aggregation during renaturation, we developed a novel application of mass spectrometry using isotopic labeling to determine the step(s) at which K97I commits to either the native or aggregated state. Interestingly, despite the early formation of a folding intermediate ensemble at an observed rate lambda(2) of 4.0 s(-1), K97I commits to folding at a significantly slower rate lambda(CF) of 0.021 s(-1). This rate of commitment to folding is in excellent agreement with the observed rate of K97I native state formation (lambda(1) = 0.018 s(-1)). K97I also commits slowly to aggregation at an observed rate lambda(CA) of 0.023 s(-1). Earlier folding species and aggregates present prior to these commitment steps are likely to be in a reversible equilibrium between monomeric folding intermediates and higher-order oligomers. Kinetic and equilibrium experimental measurements of folding and aggregation processes are consistent with a nucleation-dependent model of aggregation.
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Banky P, Newlon MG, Roy M, Garrod S, Taylor SS, Jennings PA. Isoform-specific differences between the type Ialpha and IIalpha cyclic AMP-dependent protein kinase anchoring domains revealed by solution NMR. J Biol Chem 2000; 275:35146-52. [PMID: 10899163 DOI: 10.1074/jbc.m003961200] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic AMP dependent protein kinase (PKA) is controlled, in part, by the subcellular localization of the enzyme (). Discovery of dual specificity anchoring proteins (d-AKAPs) indicates that not only is the type II, but also the type I, enzyme localized (). It appears that the type I enzyme is localized in a novel, dynamic fashion as opposed to the apparent static localization of the type II enzyme. Recently, the structure of the dimerization/docking (D/D) domain from the type II enzyme was solved (). This work revealed an X-type four-helix bundle motif with a hydrophobic patch that modulates AKAP interactions. To understand the dynamic versus static localization of PKA, multidimensional NMR techniques were used to investigate the structural features of the type I D/D domain. Our results indicate a conserved helix-turn-helix motif in the type I and type II D/D domains. However, important differences between the two domains are evident in the extreme NH(2) terminus: this region is extended in the type II domain, whereas it is helical in the type I protein. The NH(2)-terminal residues in RIIalpha contain determinants for anchoring, and the orientation and packing of this helical element in the RIalpha structure may have profound consequences in the recognition surface presented to the AKAPs.
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Heidary DK, O'Neill JC, Roy M, Jennings PA. An essential intermediate in the folding of dihydrofolate reductase. Proc Natl Acad Sci U S A 2000; 97:5866-70. [PMID: 10811909 PMCID: PMC18525 DOI: 10.1073/pnas.100547697] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The folding of Escherichia coli dihydrofolate reductase was examined at pH 7.8 and 15 degrees C by using stopped-flow fluorescence and absorbance spectroscopies. The formation of a highly fluorescent intermediate occurs with relaxation times ranging between 142 and 343 msec, whereas stopped-flow absorbance spectroscopy using methotrexate binding assays shows a distinct lag phase during these time frames for the native state. The lag in absorbance kinetics and the lack of fast-track folding events indicate that the formation of this ensemble of intermediates is an obligatory step in the folding reaction.
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Clementi C, Jennings PA, Onuchic JN. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proc Natl Acad Sci U S A 2000; 97:5871-6. [PMID: 10811910 PMCID: PMC18526 DOI: 10.1073/pnas.100547897] [Citation(s) in RCA: 187] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The overall structure of the transition-state and intermediate ensembles observed experimentally for dihydrofolate reductase and interleukin-1beta can be obtained by using simplified models that have almost no energetic frustration. The predictive power of these models suggests that, even for these very large proteins with completely different folding mechanisms and functions, real protein sequences are sufficiently well designed, and much of the structural heterogeneity observed in the intermediates and the transition-state ensembles is determined by topological effects.
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Finke JM, Roy M, Zimm BH, Jennings PA. Aggregation events occur prior to stable intermediate formation during refolding of interleukin 1beta. Biochemistry 2000; 39:575-83. [PMID: 10642182 DOI: 10.1021/bi991518m] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A point mutation, lysine 97 --> isoleucine (K97I), in a surface loop in the beta-sheet protein interleukin 1beta (IL-1beta), exhibits increased levels of inclusion body (IB) formation relative to the wild-type protein (WT) when expressed in Escherichia coli. Despite the common observation that less stable proteins are often found in IBs, K97I is more stable than WT. We examined the folding pathway of the mutant and wild-type proteins at pH 6.5 and 25 degrees C with manual-mixing and stopped-flow optical spectroscopy to determine whether changes in the properties of transiently populated species in vitro correlate with the observation of increased aggregation in vivo. The refolding reactions of the WT and K97I proteins are both described by three exponential processes. Two exponential processes characterize fast events (0.1-1.0 s) in folding while the third exponential process correlates with a slow (70 s) single pathway to and from the native state. The K97I replacement affects the earlier steps in the refolding pathway. Aggregation, absent in the WT refolding reaction, occurs in K97I above a critical protein concentration of 18 microM. This observation is consistent with an initial nucleation step mediating protein aggregation. Stopped-flow kinetic studies of the K97I aggregation process demonstrate that K97I aggregates most rapidly during the earliest refolding times, when unfolded protein conformers remain highly populated and the concentration of folding intermediates is low. Folding and aggregation studies together support a model in which the formation of stable folding intermediates afford protection against further K97I aggregation.
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Newlon MG, Roy M, Morikis D, Hausken ZE, Coghlan V, Scott JD, Jennings PA. The molecular basis for protein kinase A anchoring revealed by solution NMR. NATURE STRUCTURAL BIOLOGY 1999; 6:222-7. [PMID: 10074940 DOI: 10.1038/6663] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Compartmentalization of signal transduction enzymes into signaling complexes is an important mechanism to ensure the specificity of intracellular events. Formation of these complexes is mediated by specialized protein motifs that participate in protein-protein interactions. The adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) is localized through interaction of the regulatory (R) subunit dimer with A-kinase-anchoring proteins (AKAPs). We now report the solution structure of the type II PKA R-subunit fragment RIIalpha(1-44), which encompasses both the AKAP-binding and dimerization interfaces. This structure incorporates an X-type four-helix bundle dimerization motif with an extended hydrophobic face that is necessary for high-affinity AKAP binding. NMR data on the complex between RIIalpha(1-44) and an AKAP fragment reveals extensive contacts between the two proteins. Interestingly, this same dimerization motif is present in other signaling molecules, the S100 family. Therefore, the X-type four-helix bundle may represent a conserved fold for protein-protein interactions in signal transduction.
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