scholarly journals FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W499-W502 ◽  
Author(s):  
H. K. Saini ◽  
D. Fischer
Keyword(s):  
Functional Analysis ◽  
Fold Recognition ◽  
Sequence Structure ◽  
Recognition Sequence

scholarly journals M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target

Microbiology ◽  
2009 ◽  
Vol 155 (4) ◽  
pp. 1111-1121 ◽  
Author(s):  
Beata Furmanek-Blaszk ◽  
Robert Boratynski ◽  
Natalia Zolcinska ◽  
Marian Sektas
Keyword(s):  
Functional Analysis ◽  
Divalent Cations ◽  
Restriction Enzymes ◽  
Bacterial Cells ◽  
Recognition Sequence ◽  
Moraxella Bovis ◽  
Chromatographic Procedure ◽  
Methylation Activity ◽  
Restriction Modification ◽  
Endonuclease Gene

Methylation of a base in a specific DNA sequence protects the DNA from nucleolytic cleavage by restriction enzymes recognizing the same sequence. The MboII restriction–modification (R–M) system of Moraxella bovis ATCC 10900 consists of a restriction endonuclease gene and two methyltransferase genes. The enzymes encoded by this system recognize an asymmetrical sequence 5′-GAAGA-3′/3′-CTTCT-5′. M1.MboII modifies the last adenine in the recognition sequence 5′-GAAGA-3′ to N 6-methyladenine. A second methylase, M2.MboII, was cloned and purified to electrophoretic homogeneity using a four-step chromatographic procedure. It was demonstrated that M2.MboII modifies the internal cytosine in the recognition sequence 3′-CTTCT-5′, yielding N 4-methylcytosine, and moreover is able to methylate single-stranded DNA. The protein exists in solution as a monomer of molecular mass 30 000±1000 Da under denaturing conditions. Divalent cations (Ca2+, Mg2+, Mn2+ and Zn2+) inhibit M2.MboII methylation activity. It was found that the isomethylomer M2.NcuI from Neisseria cuniculi ATCC 14688 behaves in the same manner. Functional analysis showed that the complete MboII R–M system, consisting of two methyltransferases genes and the mboIIR gene, is the most stable and the least harmful to bacterial cells.

Comparative sequence, structure and functional analysis of Skp protein, a molecular chaperone among members of Pasteurellaceae and its homologues in Gram-negative bacteria

Meta Gene ◽  
2020 ◽  
Vol 24 ◽  
pp. 100680 ◽  
Author(s):  
Rajamanikandan Sundarraj ◽  
Nihar Nalini Mohanty ◽  
Revanaiah Yogisharadhya ◽  
Jeyaraman Jeyakanthan ◽  
Awadesh Prajapati ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Molecular Chaperone ◽  
Protein A ◽  
Gram Negative Bacteria ◽  
Sequence Structure ◽  
Gram Negative ◽  
Comparative Sequence

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre

2008 ◽  
Vol 70 (3) ◽  
pp. 611-625 ◽  
Author(s):  
Riccardo M. Bennett‐Lovsey ◽  
Alex D. Herbert ◽  
Michael J. E. Sternberg ◽  
Lawrence A. Kelley
Keyword(s):  
Fold Recognition ◽  
Sequence Structure ◽  
Structure Space

Fold recognition and accurate sequence-structure alignment of sequences directing β-sheet proteins

2006 ◽  
Vol 63 (4) ◽  
pp. 976-985 ◽  
Author(s):  
Andrew V. McDonnell ◽  
Matthew Menke ◽  
Nathan Palmer ◽  
Jonathan King ◽  
Lenore Cowen ◽  
...  
Keyword(s):  
Fold Recognition ◽  
Structure Alignment ◽  
Sequence Structure ◽  
Β Sheet

Case Formulation and Design of Behavioral Treatment Programs

2003 ◽  
Vol 19 (3) ◽  
pp. 164-174 ◽  
Author(s):  
Stephen N. Haynes ◽  
Andrew E. Williams
Keyword(s):  
Functional Analysis ◽  
Behavior Problems ◽  
Behavioral Treatment ◽  
Clinical Case ◽  
Relative Magnitude ◽  
Mechanisms Of Action ◽  
Treatment Programs ◽  
Case Formulation ◽  
Functional Relations ◽  
Causal Variables

Summary: We review the rationale for behavioral clinical case formulations and emphasize the role of the functional analysis in the design of individualized treatments. Standardized treatments may not be optimally effective for clients who have multiple behavior problems. These problems can affect each other in complex ways and each behavior problem can be influenced by multiple, interacting causal variables. The mechanisms of action of standardized treatments may not always address the most important causal variables for a client's behavior problems. The functional analysis integrates judgments about the client's behavior problems, important causal variables, and functional relations among variables. The functional analysis aids treatment decisions by helping the clinician estimate the relative magnitude of effect of each causal variable on the client's behavior problems, so that the most effective treatments can be selected. The parameters of, and issues associated with, a functional analysis and Functional Analytic Clinical Case Models (FACCM) are illustrated with a clinical case. The task of selecting the best treatment for a client is complicated because treatments differ in their level of specificity and have unequally weighted mechanisms of action. Further, a treatment's mechanism of action is often unknown.

The Social Order Yields to Functional Analysis

1958 ◽  
Vol 3 (6) ◽  
pp. 158-160
Author(s):  
LAWRENCE SCHLESINGER
Keyword(s):  
Functional Analysis ◽  
Social Order ◽  
The Social
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