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Artikel ; Online: Helmet and Pad Removal for Football Head and Neck Injuries.

Mills, Ralph L / Johnston, James R / Harter, Caitlyn C

2023 Band 108, Heft 3, Seite(n) Online

Mesh-Begriff(e)	Humans ; Football ; Head Protective Devices ; Neck Injuries/therapy
Sprache	Englisch
Erscheinungsdatum	2023-09-19
Erscheinungsland	United States
Dokumenttyp	Letter ; Comment
ZDB-ID	412694-4
ISSN	1532-0650 ; 0002-838X ; 0572-3612
ISSN (online)	1532-0650
ISSN	0002-838X ; 0572-3612
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily.

Mills, Caitlyn L / Yin, Pengcheng / Leifer, Becky / Ferrins, Lori / O'Doherty, George A / Beuning, Penny J / Ondrechen, Mary Jo

ACS chemical biology

2022 Band 17, Heft 2, Seite(n) 395–403

Abstract: Members of the Crotonase superfamily, a mechanistically diverse family of proteins that share a conserved quaternary structure, can often catalyze more than one reaction. However, the spectrum of activity for its members has not been well studied. We ... ...

Abstract	Members of the Crotonase superfamily, a mechanistically diverse family of proteins that share a conserved quaternary structure, can often catalyze more than one reaction. However, the spectrum of activity for its members has not been well studied. We report on measured crotonase and hydrolase activity for eight structural genomics (SG) proteins from the Crotonase superfamily plus two previously characterized proteins, intended as controls: human enoyl CoA hydratase (ECH) and
Mesh-Begriff(e)	Catalysis ; Databases, Protein ; Enoyl-CoA Hydratase/chemistry ; Enoyl-CoA Hydratase/metabolism ; Genomics ; Humans ; Hydrolases/chemistry
Chemische Substanzen	Hydrolases (EC 3.-) ; Enoyl-CoA Hydratase (EC 4.2.1.17)
Sprache	Englisch
Erscheinungsdatum	2022-01-21
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.1c00842
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Biochemical functional predictions for protein structures of unknown or uncertain function.

Mills, Caitlyn L / Beuning, Penny J / Ondrechen, Mary Jo

Computational and structural biotechnology journal

2015 Band 13, Seite(n) 182–191

Abstract: With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. ...

Abstract	With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
Sprache	Englisch
Erscheinungsdatum	2015-02-18
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article ; Review
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2015.02.003
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis.

MacPherson, Derek J / Mills, Caitlyn L / Ondrechen, Mary Jo / Hardy, Jeanne A

The Journal of biological chemistry

2018 Band 294, Heft 1, Seite(n) 71–88

Abstract: Caspases are cysteine-aspartic proteases involved in the regulation of programmed cell death (apoptosis) and a number of other biological processes. Despite overall similarities in structure and active-site composition, caspases show striking selectivity ...

Abstract	Caspases are cysteine-aspartic proteases involved in the regulation of programmed cell death (apoptosis) and a number of other biological processes. Despite overall similarities in structure and active-site composition, caspases show striking selectivity for particular protein substrates. Exosites are emerging as one of the mechanisms by which caspases can recruit, engage, and orient these substrates for proper hydrolysis. Following computational analyses and database searches for candidate exosites, we utilized site-directed mutagenesis to identify a new exosite in caspase-6 at the hinge between the disordered N-terminal domain (NTD), residues 23-45, and core of the caspase-6 structure. We observed that substitutions of the tri-arginine patch Arg-42-Arg-44 or the R44K cancer-associated mutation in caspase-6 markedly alter its rates of protein substrate hydrolysis. Notably, turnover of protein substrates but not of short peptide substrates was affected by these exosite alterations, underscoring the importance of this region for protein substrate recruitment. Hydrogen-deuterium exchange MS-mediated interrogation of the intrinsic dynamics of these enzymes suggested the presence of a substrate-binding platform encompassed by the NTD and the 240's region (containing residues 236-246), which serves as a general exosite for caspase-6-specific substrate recruitment. In summary, we have identified an exosite on caspase-6 that is critical for protein substrate recognition and turnover and therefore highly relevant for diseases such as cancer in which caspase-6-mediated apoptosis is often disrupted, and in neurodegeneration in which caspase-6 plays a central role.
Mesh-Begriff(e)	Amino Acid Substitution ; Arginine/chemistry ; Arginine/genetics ; Arginine/metabolism ; Caspase 6/chemistry ; Caspase 6/genetics ; Caspase 6/metabolism ; Humans ; Hydrolysis ; Mutation, Missense ; Neoplasm Proteins/chemistry ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasms/enzymology ; Neoplasms/genetics ; Neoplasms/pathology ; Neurodegenerative Diseases/enzymology ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Protein Domains
Chemische Substanzen	Neoplasm Proteins ; Arginine (94ZLA3W45F) ; CASP6 protein, human (EC 3.4.22.-) ; Caspase 6 (EC 3.4.22.-)
Sprache	Englisch
Erscheinungsdatum	2018-11-12
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.005914
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Biochemical functional predictions for protein structures of unknown or uncertain function

Caitlyn L. Mills / Penny J. Beuning / Mary Jo Ondrechen

Computational and Structural Biotechnology Journal, Vol 13, Iss C, Pp 182-

2015 Band 191

Abstract	With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
Schlagwörter	Structural genomics ; Protein function prediction ; Local structure methods ; Computational chemistry ; Biotechnology ; TP248.13-248.65
Sprache	Englisch
Erscheinungsdatum	2015-01-01T00:00:00Z
Verlag	Elsevier
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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Artikel: PCV7- and PCV10-Vaccinated Otitis-Prone Children in New Zealand Have Similar Pneumococcal and

de Gier, Camilla / Granland, Caitlyn M / Pickering, Janessa L / Walls, Tony / Bhuiyan, Mejbah / Mills, Nikki / Richmond, Peter C / Best, Emma J / Thornton, Ruth B / Kirkham, Lea-Ann S

Vaccines

2019 Band 7, Heft 1

Abstract: Otitis media (OM) is a major reason for antibiotic consumption and surgery in children. Nasopharyngeal carriage of otopathogens, ...

Abstract	Otitis media (OM) is a major reason for antibiotic consumption and surgery in children. Nasopharyngeal carriage of otopathogens,
Sprache	Englisch
Erscheinungsdatum	2019-01-31
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines7010014
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Functional classification of protein structures by local structure matching in graph representation.

Mills, Caitlyn L / Garg, Rohan / Lee, Joslynn S / Tian, Liang / Suciu, Alexandru / Cooperman, Gene D / Beuning, Penny J / Ondrechen, Mary Jo

Protein science : a publication of the Protein Society

2018 Band 27, Heft 6, Seite(n) 1125–1135

Abstract: As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by Structural Genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to ... ...

Abstract	As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by Structural Genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, Structurally Aligned Local Sites of Activity (SALSA), using the Ribulose Phosphate Binding Barrel (RPBB), 6-Hairpin Glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community.
Mesh-Begriff(e)	Catalytic Domain ; Computational Biology ; Glycoside Hydrolases ; Lectins/chemistry ; Pentoses/chemistry ; Protein Conformation ; Proteins/chemistry
Chemische Substanzen	Lectins ; Pentoses ; Proteins ; ribulose (5556-48-9) ; Glycoside Hydrolases (EC 3.2.1.-)
Sprache	Englisch
Erscheinungsdatum	2018-04-27
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3416
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases.

Parasuram, Ramya / Mills, Caitlyn L / Wang, Zhouxi / Somasundaram, Saroja / Beuning, Penny J / Ondrechen, Mary Jo

Methods (San Diego, Calif.)

2016 Band 93, Seite(n) 51–63

Abstract: ... L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein ...

Abstract	Thousands of protein structures of unknown or uncertain function have been reported as a result of high-throughput structure determination techniques developed by Structural Genomics (SG) projects. However, many of the putative functional assignments of these SG proteins in the Protein Data Bank (PDB) are incorrect. While high-throughput biochemical screening techniques have provided valuable functional information for limited sets of SG proteins, the biochemical functions for most SG proteins are still unknown or uncertain. Therefore, computational methods for the reliable prediction of protein function from structure can add tremendous value to the existing SG data. In this article, we show how computational methods may be used to predict the function of SG proteins, using examples from the six-hairpin glycosidase (6-HG) and the concanavalin A-like lectin/glucanase (CAL/G) superfamilies. Using a set of predicted functional residues, obtained from computed electrostatic and chemical properties for each protein structure, it is shown that these superfamilies may be sorted into functional families according to biochemical function. Within these superfamilies, a total of 18 SG proteins were analyzed according to their predicted, local functional sites: 13 from the 6-HG superfamily, five from the CAL/G superfamily. Within the 6-HG superfamily, an uncharacterized protein BACOVA_03626 from Bacteroides ovatus (PDB 3ON6) and a hypothetical protein BT3781 from Bacteroides thetaiotaomicron (PDB 2P0V) are shown to have very strong active site matches with exo-α-1,6-mannosidases, thus likely possessing this function. Also in this superfamily, it is shown that protein BH0842, a putative glycoside hydrolase from Bacillus halodurans (PDB 2RDY), has a predicted active site that matches well with a known α-L-galactosidase. In the CAL/G superfamily, an uncharacterized glycosyl hydrolase family 16 protein from Mycobacterium smegmatis (PDB 3RQ0) is shown to have local structural similarity at the predicted active site with the known members of the GH16 family, with the closest match to the endoglucanase subfamily. The method discussed herein can predict whether an SG protein is correctly or incorrectly annotated and can sometimes provide a reliable functional annotation. Examples of application of the method across folds, comparing active sites between two proteins of different structural folds, are also given.
Mesh-Begriff(e)	Computational Biology/methods ; Databases, Protein ; Forecasting ; Glycoside Hydrolases/chemistry ; Glycoside Hydrolases/physiology ; Protein Structure, Secondary ; Proteins/chemistry ; Proteins/physiology
Chemische Substanzen	Proteins ; Glycoside Hydrolases (EC 3.2.1.-)
Sprache	Englisch
Erscheinungsdatum	2016-01-15
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2015.11.010
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Biochemical functional predictions for protein structures of unknown or uncertain function

Mills, Caitlyn L / Mary Jo Ondrechen / Penny J. Beuning

Computational and Structural Biotechnology Journal. 2015, v. 13

2015

Abstract	With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI), COMputational BRidges to EXperiments (COMBREX), and the Critical Assessment of Function Annotation (CAFA), are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.
Schlagwörter	amino acid sequences ; biotechnology ; catalytic activity ; genomics ; prediction ; proteins ; sequence analysis
Sprache	Englisch
Umfang	p. 182-191.
Erscheinungsort	Elsevier B.V.
Dokumenttyp	Artikel
ISSN	2001-0370
DOI	10.1016/j.csbj.2015.02.003
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: PCV7- and PCV10-Vaccinated Otitis-Prone Children in New Zealand Have Similar Pneumococcal and Haemophilus influenzae Densities in Their Nasopharynx and Middle Ear

Camilla de Gier / Caitlyn M. Granland / Janessa L. Pickering / Tony Walls / Mejbah Bhuiyan / Nikki Mills / Peter C. Richmond / Emma J. Best / Ruth B. Thornton / Lea-Ann S. Kirkham

Vaccines, Vol 7, Iss 1, p

2019 Band 14

Abstract: Otitis media (OM) is a major reason for antibiotic consumption and surgery in children. Nasopharyngeal carriage of otopathogens, Streptococcus pneumoniae and nontypeable Haemophilus influenzae (NTHi), is a prerequisite for development of OM, and ... ...

Abstract	Otitis media (OM) is a major reason for antibiotic consumption and surgery in children. Nasopharyngeal carriage of otopathogens, Streptococcus pneumoniae and nontypeable Haemophilus influenzae (NTHi), is a prerequisite for development of OM, and increased nasopharyngeal otopathogen density correlates with disease onset. Vaccines can reduce or eliminate otopathogen carriage, as demonstrated for pneumococcal serotypes included in pneumococcal conjugate vaccines (PCV). The 10-valent PCV (PCV10) includes an NTHi carrier protein, and in 2011 superseded 7-valent PCV on the New Zealand Immunisation Program. Data are conflicting on whether PCV10 provides protection against NTHi carriage or disease. Assessing this in otitis-prone cohorts is important for OM prevention. We compared otopathogen density in the nasopharynx and middle ear of New Zealand PCV7-vaccinated and PCV10-vaccinated otitis-prone and non-otitis-prone children to determine PCV10 impact on NTHi and S. pneumoniae carriage. We applied qPCR to specimens collected from 217 PCV7-vaccinated children (147 otitis-prone and 70 non-otitis-prone) and 240 PCV10-vaccinated children (178 otitis-prone and 62 non-otitis-prone). After correcting for age and day-care attendance, no difference was observed between NTHi density in the nasopharynx of PCV7-vaccinated versus PCV10-vaccinated otitis-prone ( p = 0.563) or non-otitis-prone ( p = 0.513) children. In contrast, pneumococcal nasopharyngeal density was higher in PCV10-vaccinated otitis-prone children than PCV7-vaccinated otitis-prone children ( p = 0.003). There was no difference in otopathogen density in middle ear effusion from PCV7-vaccinated versus PCV10-vaccinated otitis-prone children (NTHi p = 0.918; S. pneumoniae p = 0.415). When pneumococcal carriage was assessed by vaccine serotypes (VT) and non-vaccine serotypes (NVT), there was no difference in VT density ( p = 0.546) or NVT density ( p = 0.315) between all PCV7-vaccinated versus all PCV10-vaccinated children. In summary, PCV10 did not reduce NTHi density ...
Schlagwörter	carriage density ; nasopharynx ; New Zealand ; otitis media ; pneumococcal conjugate vaccine ; NTHi ; qPCR ; Medicine ; R
Thema/Rubrik (Code)	360
Sprache	Englisch
Erscheinungsdatum	2019-01-01T00:00:00Z
Verlag	MDPI AG
Dokumenttyp	Artikel ; Online
Datenquelle	BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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