Tonal interface to MacroMolecules (TIMMol)

Cordes, Timothy J.; Carlson, Coby B.; Forest, Katrina T.

doi:10.1002/bmb.20183

Cited by 4 publications

(4 citation statements)

References 27 publications

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“…The seven N-terminal residues, residues 80 to 84, and the C-terminal amino acid were not well ordered and were not included in the final model. Structure analysis was carried out using the tonal molecular modeling program TimMol (8) and PyMOL (10). Protein interface areas were calculated using the PISA web server (21).…”

Section: Methodsmentioning

confidence: 99%

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

et al. 2011

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Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prevents the growth of P. aeruginosa.Pseudomonas aeruginosa is a ubiquitous, Gram-negative opportunistic pathogen that is a leading source of morbidity and mortality for individuals with compromised immune systems or cystic fibrosis. P. aeruginosa switches from an environmental organism to a pathogen through the regulation and elaboration of multiple virulence factors. Virulence factor regulator (Vfr) is a central player in a transcriptional cascade that controls this transition.Vfr is a 24-kDa protein belonging to the winged-helix family of transcription regulators (40). Vfr positively regulates quorum sensing by promoting the transcription of lasR, upregulates transcription of the type III secretion system, represses flagellar gene transcription, and positively regulates twitching motility (1, 2, 9, 41). Vfr binds cyclic adenosine 3Ј5Ј monophosphate (cyclic AMP [cAMP]) in vitro with a dissociation constant of 1.6 M (39). Deletion of both cytoplasmic P. aeruginosa adenyl cyclases results in a transcription profile similar to a vfr deletion (41). Furthermore, like the strain carrying the vfr deletion, the double adenyl cyclase mutant has reduced virulence compared to the wild-type strain in a mouse pneumonia model (38). Thus, cAMP is a biologically relevant ligand for Vfr in vivo.The amino acid sequence of Vfr is 67% identical to that of cAMP receptor protein (CRP) from Escherichia coli (40), a long-standing model for the study of transcription regulation and a structurally well-characterized protein (22). When overexpressed, Vfr complements the ␤-galactosidase and tryptophanase-deficient phenotypes of a crp deletion in E. coli (40). Conversely, CRP expressed in a vfr deletion strain of P. aeruginosa promotes sub-wild-type levels of lasR transcription. However, CRP is unable to rescue the protease-or exotoxin A-deficient phenotypes of the vfr mutant (40). Recent work suggests that this discrepancy might be due at least in part to cAMPindependent regulation at the lasR promoter (15).Mounting evidence supports a model for CRP function in which a dimer of CRP binds a cAMP ligand in the N-terminal domain of each monomer to achieve the protein conformation needed for high-affinity specific DNA binding and DNA bending that precedes transcriptional activation. CRP demonstrates low affinity for specific DNA sequences, with a K d of ϳ10 Ϫ4 M, in the absence of cAMP (16). Its specificity and affinity for its promoter sites increase to 10 Ϫ7 to 10 Ϫ8 M in cAMP concentrations...

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Section: Methodsmentioning

confidence: 99%

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

et al. 2011

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“…Academics with Visual impairment teach courses that are traditionally taught by sighted teachers such as Biomedical Engineering (Greenvall et al, 2021). In addition, software and systems have been developed to facilitate collaboration between sighted and non-sighted researchers in fields like Molecular Biology (Cordes et al, 2008).…”

Section: The Significance Of the Articlementioning

confidence: 99%

Evaluation of Qualitative Data Analysis Software by a Visually Impaired Researcher: An Autoethnographic Study

Emara

2023

International Journal of Qualitative Methods

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Although computational methods facilitate research studies greatly, academics with visual impairment cannot utilize these tools to their maximum potential. Not only do computational research methods themselves have many shortcomings, but the needs and problems encountered by researchers with visual impairment in using these tools are not identified. In particular, the use of qualitative data analysis software (Q-DAS) by researchers with visual impairment has not been thoroughly examined. Thus, the current article addresses the benefits that visually impaired researchers can gain from employing commercial Q-DAS software packages in analyzing qualitative data. Further, Q-DAS problems that researchers with visual impairments experience are discussed. In addition, the article proposes solutions by which Q-DAS utilization in studies performed by/for the visual impairment community could improve. The article has many significant contributions, not only for scholars with visual impairment but also for elderly scientists whose vision declines over time. The article addresses this topic through critical disability studies.

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“…Many methods have been developed to teach students about protein structure and the forces that govern it. These include two‐dimensional presentations in textbooks and slides; physical models (for example, [1, 2]); audio feedback [3]; and, quite frequently, computer‐aided visualization (for an extensive library of examples, see http://www.molviz.org). Visualization typically takes the form of two‐dimensional displays, where interactive controls allow the user to explore and experience the three‐dimensional structure of the protein under study.…”

mentioning

confidence: 99%

“…Visualization typically takes the form of two‐dimensional displays, where interactive controls allow the user to explore and experience the three‐dimensional structure of the protein under study. A large number of software programs have been developed for this purpose (including [4, 5], and http://www.jmol.org); these have been received positively by students [3, 4] and their use has been correlated with increased understanding of key elements of protein biochemistry [1, 6].…”

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confidence: 99%

Evaluation of software for introducing protein structure

White¹,

Kahriman²,

Luberice³

et al. 2010

Biochem Molecular Bio Educ

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Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated with student learning, it is quite challenging to develop visualizations that allow students to interactively observe the effects of altered amino acid sequence on protein structure. A software simulation, the protein investigator (PI), has been developed to specifically facilitate this type of exploration. When using the PI, students enter or edit an amino acid sequence; the software then simulates its folding in two dimensions using the major forces involved in protein structure. This study explores freshman undergraduate students' use of visualization and simulation when learning about protein structure. It also evaluates some of the learning outcomes from these two approaches. Our results show that simulation leads to similar learning outcomes as visualization. Because simulation allows a more interactive exploration, a combination of the two approaches may be an effective approach to introducing the basic principles of protein structure.Keywords: Undergraduate, protein structure, visualization, simulation, evaluation.Proteins are a major component of all cells and are responsible for carrying out many of the functions of living organisms. A protein's function is determined primarily by its structure, which is largely determined by its amino acid sequence; this process is mediated by a variety of covalent and noncovalent interactions between the amino acids. Mutations can act by causing changes in the amino acid sequence of proteins that can lead to alterations in function, which may have effects on phenotype. An understanding of these issues is an essential part of understanding modern molecular biology and is a key component of biology and biochemistry courses from high school through graduate school, albeit at different levels of precision.Many methods have been developed to teach students about protein structure and the forces that govern it. These include two-dimensional presentations in textbooks and slides; physical models (for example, [1, 2]); audio feedback [3]; and, quite frequently, computer-aided visualization (for an extensive library of examples, see molviz.org). Visualization typically takes the form of twodimensional displays, where interactive controls allow the user to explore and experience the three-dimensional structure of the protein under study. A large number of software programs have been developed for this purpose (including [4,5], and www.jmol.org); these have been received positively by students [3,4] and their use has been correlated with increased understanding of key elements of protein biochemistry [1,6].One important use of these visualizations is to have students develop hypotheses about the interactions they observe and the possi...

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Tonal interface to MacroMolecules (TIMMol)

Cited by 4 publications

References 27 publications

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator

Evaluation of Qualitative Data Analysis Software by a Visually Impaired Researcher: An Autoethnographic Study

Evaluation of software for introducing protein structure

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