Results 11 - 20
of
53
SAXS Study of the PIR Domain from the Grb14 Molecular Adaptor: A Natively Unfolded Protein with a Transient Structure Primer?
"... ABSTRACT Grb14 belongs to the Grb7 family of adapters and was identified as a negative regulator of insulin signal transduction. Between the PH (pleckstrin homology) and SH2 (Src homology 2) domains is a new binding domain implicated in the interaction with receptor tyrosine kinases called PIR (phos ..."
Abstract
-
Cited by 4 (0 self)
- Add to MetaCart
(Show Context)
ABSTRACT Grb14 belongs to the Grb7 family of adapters and was identified as a negative regulator of insulin signal transduction. Between the PH (pleckstrin homology) and SH2 (Src homology 2) domains is a new binding domain implicated in the interaction with receptor tyrosine kinases called PIR (phosphorylated insulin receptor interaction region). Both PIR and SH2 domains interact with the insulin receptor, but their relative role varies considering the member of the Grb7 family and the tyrosine kinase receptor. In the case of Grb14, PIR is the main binding domain and is sufficient to inhibit the insulin receptor kinase activity. We have proposed, on the basis of NMR measurements, that PIR lacks ordered structure and presents a high flexibility, although remaining fully active. To complement this first study, we have used small-angle x-ray scattering in solution together with a modeling approach representing the PIR domain as a chain of pseudo residues. Circular dichroism experiments were also performed in the presence of variable amounts of trifluoroethanol. These observations, together with an ensemble of sequence analyses and previous NMR results, all support the view of PIR as essentially unstructured but with a potentially structured short stretch encompassing residues 399–407. This stretch, which may be only structured transiently in the isolated molecule, could play a major role in Grb14 PIR binding to a biological partner by undergoing a structural transition.
Biophysical characterization of the unstructured cytoplasmic domain of the human neuronal adhesion protein neuroligin 3
- Biophys. J
, 2008
"... ABSTRACT Cholinesterase-like adhesion molecules (CLAMs) are a family of neuronal cell adhesion molecules with important roles in synaptogenesis, and in maintaining structural and functional integrity of the nervous system. Our earlier study on the cytoplasmic domain of one of these CLAMs, the Drosop ..."
Abstract
-
Cited by 2 (0 self)
- Add to MetaCart
(Show Context)
ABSTRACT Cholinesterase-like adhesion molecules (CLAMs) are a family of neuronal cell adhesion molecules with important roles in synaptogenesis, and in maintaining structural and functional integrity of the nervous system. Our earlier study on the cytoplasmic domain of one of these CLAMs, the Drosophila protein, gliotactin, showed that it is intrinsically unstructured in vitro. Bioinformatic analysis suggested that the cytoplasmic domains of other CLAMs are also intrinsically unstructured, even though they bear no sequence homology to each other or to any known protein. In this study, we overexpress and purify the cytoplasmic domain of human neuroligin 3, notwithstanding its high sensitivity to the Escherichia coli endogenous proteases that cause its rapid degradation. Using bioinformatic analysis, sensitivity to proteases, size exclusion chromatography, fluorescence correlation spectroscopy, analytical ultracentrifugation, small angle x-ray scattering, circular dichroism, electron spin resonance, and nuclear magnetic resonance, we show that the cytoplasmic domain of human neuroligin 3 is intrinsically unstructured. However, several of these techniques indicate that it is not fully extended, but becomes significantly more extended under denaturing conditions.
The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint
, 2011
"... genes ..."
(Show Context)
Determination of Protein Structures—A Series of Fortunate Events
, 2008
"... ABSTRACT Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success ..."
Abstract
-
Cited by 2 (0 self)
- Add to MetaCart
(Show Context)
ABSTRACT Determination of a macromolecular structure using x-ray diffraction is a multistep process that involves a plethora of techniques involving molecular biology, bioinformatics, and physical sciences. Counterintuitively, the success of any or all individual steps does not guarantee the success of the overall process. This review examines the difficulties presented by each step on the path from a gene to the final publication, together with certain lucky (or unlucky) circumstances that can affect the velocity along that path.
5 Prediction of Intrinsic Disorder and Its Use in Functional Proteomics
"... The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising. Research is often focused on a structural characterization of a given protein, looking for several key features. However, ID proteins with their dynamic structures that interconvert on a number of time-s ..."
Abstract
-
Cited by 1 (0 self)
- Add to MetaCart
(Show Context)
The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising. Research is often focused on a structural characterization of a given protein, looking for several key features. However, ID proteins with their dynamic structures that interconvert on a number of time-scales are difficult targets for the majority of traditional biophysical and biochemical techniques. Structural and functional analyses of these proteins can be significantly aided by disorder predictions. The current advances in the prediction of ID proteins and the use of protein disorder prediction in the fields of molecular biology and bioinformatics are briefly overviewed herein. A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes. Key Words: Intrinsically disordered protein; natively unfolded protein; intrinsically unstructured protein; protein flexibility; disorder prediction; protein function.
Review What Macromolecular Crowding Can Do to a Protein
, 2014
"... Abstract: The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the ..."
Abstract
-
Cited by 1 (0 self)
- Add to MetaCart
Abstract: The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life ” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is
unknown title
"... Certain organisms are able to survive almost complete loss of their internal water, entering a state of suspended animation called anhydrobiosis. When water becomes available again, the organism revives and resumes its normal activities. These organisms have ..."
Abstract
- Add to MetaCart
(Show Context)
Certain organisms are able to survive almost complete loss of their internal water, entering a state of suspended animation called anhydrobiosis. When water becomes available again, the organism revives and resumes its normal activities. These organisms have
Structural bioinformatics Prediction of unfolded segments in a protein sequence based
"... Motivation: Partially and wholly unstructured proteins have now been identified in all kingdoms of life—more commonly in eukaryotic organ-isms. This intrinsic disorder is related to certain critical functions. Apart from their fundamental interest, unstructured regions in proteins may prevent crysta ..."
Abstract
- Add to MetaCart
(Show Context)
Motivation: Partially and wholly unstructured proteins have now been identified in all kingdoms of life—more commonly in eukaryotic organ-isms. This intrinsic disorder is related to certain critical functions. Apart from their fundamental interest, unstructured regions in proteins may prevent crystallization. Therefore, the prediction of disordered regions is an important aspect for the understanding of protein function, but may also help to devise genetic constructs. Results: In this paper we present a computational tool for the detec-tion of unstructured regions in proteins based on two properties of unfolded fragments: (1) disordered regions have a biased composition and (2) they usually contain either small or no hydrophobic clusters. In order to quantify these two facts we first calculate the amino acid distributions in structured and unstructured regions. Using this dis-tribution, we calculate for a given sequence fragment the probability to be part of either a structured or an unstructured region. For each amino acid, the distance to the nearest hydrophobic cluster is also computed. Using these three values along a protein sequence allows us to predict unstructured regions, with very simple rules. This method requires only the primary sequence, and no multiple alignment, which makes it an adequate method for orphan proteins.
Declaration
"... I declare that this thesis is my own, unaided work. It is being submitted for the degree of ..."
Abstract
- Add to MetaCart
I declare that this thesis is my own, unaided work. It is being submitted for the degree of
