| 1. |
- Shu, Nanjiang, 1981-
(författare)
-
Prediction of zinc-binding sites in proteins and efficient protein structure description and comparison
- 2008
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A large number of proteins require certain metals to stabilize their structures or to function properly. About one third of all proteins in the Protein Data Bank (PDB) contain metals and it is estimated that approximately the same proportion of all proteins are metalloproteins. Zinc, the second most abundant transition metal found in eukaryotic organisms, plays key roles, mainly structural and catalytic, in many biological functions. Predicting whether a protein binds zinc and even the accurate location of binding sites is important when investigating the function of an experimentally uncharacterized protein. Describing and comparing protein structures with both efficiency and accuracy are essential for systematic annotation of functional properties of proteins, be it on an individual or on a genome scale. Dozens of structure comparison methods have been developed in the past decades. In recent years, several research groups have endeavoured in developing methods for fast comparison of protein structures by representing the three-dimensional (3D) protein structures as one-dimensional (1D) geometrical strings based on the shape symbols of clustered regions of φ/ψ torsion angle pairs of the polypeptide backbones. These 1D geometrical strings, shape strings, are as compact as 1D secondary structures but carry more elaborate structural information in loop regions and thus are more suitable for fast structure database searching, classification of loop regions and evaluation of model structures. In this thesis, a new method for predicting zinc-binding sites in proteins from amino acid sequences is described. This method predicts zinc-binding Cys, His, Asp and Glu (the four most common zinc-binding residues) with 75% precision (86% for Cys and His only) at 50% recall according to a solid 5-fold cross-validation on a non-redundant set of the PDB chains containing 2727 unique chains, of which 235 bind to zinc. This method predicts zinc-binding Cys and His with about 10% higher precision at different recall levels compared to a previously published method. In addition, different methods for describing and comparing protein structures are reviewed. Some recently developed methods based on 1D geometrical representation of backbone structures are emphasized and analyzed in details.
|
|
| 2. |
|
|
| 3. |
- Herman Moreno, Maria Dolores, 1974-
(författare)
-
Structural studies of proteins in apoptosis and lipid signaling
- 2008
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Signaling pathways control the fate of the cell. For example, they promote cell survival or commit the cell to death (apoptosis) in response to cell injury or developmental stimuli, decisions, which are vital for the proper development and functioning of metazoan. Tight control of such pathways is essential; dysregulation of apoptosis can disrupt the delicate balance between cell proliferation and cell death ending up in pathological processes, including cancer, autoimmunity diseases, inflammatory diseases, or degenerative disorders. We have used a structural genomic approach to study the structure and function of key proteins involved in apoptosis and lipid signaling: the antiapoptotic Bcl-2 family member Bfl-1 in complex with a Bim peptide, the BIR domains of the Inhibitor of Apoptosis (IAP) family members, cIAP2 and NAIP and the a lipid kinase YegS. The structural analysis of the apoptosis regulatory proteins has revealed important information on the structural determinants for recognition of interacting proteins, which can now assist in the development of therapeutic drugs for human diseases. The structural and complementing biochemical studies of the lipid kinase YegS have reveled the first detailed information on a lipid kinase and explained important aspects of its structure-function relationship. Finally, one subject of this work aim to solve what is arguably the most challenging problem in structural projects – to obtain a high production level of proteins suitable for structural studies. We have developed a highthroughput protein solubility screening, the colony filtration (CoFi) blot, which allows soluble clones to be identified from large libraries of protein variants and now constitute a powerful tool for solving difficult protein production problems.
|
|
| 4. |
- Niegowski, Damian, 1978-, et al.
(författare)
-
Structural basis for synthesis of inflammatory mediators by human leukotriene C4 synthase
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 448:7153, s. 613-616
-
Tidskriftsartikel (refereegranskat)abstract
- Cysteinyl leukotrienes are key mediators in inflammation and have an important role in acute and chronic inflammatory diseases of the cardiovascular and respiratory systems, in particular bronchial asthma. In the biosynthesis of cysteinyl leukotrienes, conversion of arachidonic acid forms the unstable epoxide leukotriene A4 (LTA4). This intermediate is conjugated with glutathione (GSH) to produce leukotriene C4 (LTC4) in a reaction catalysed by LTC4 synthase1: this eaction is the key step in cysteinyl leukotriene formation. Here we present the rystal structure of the human LTC4 synthase in its apo and GSH-complexed forms to 2.00 and 2.15 A ̊resolution, respectively. The structure reveals a homotrimer, here each monomer is composed of four transmembrane segments. The structure of the enzyme in complex with substrate reveals that the active site enforces a orseshoe-shaped conformation on GSH, and effectively positions the thiol group or activation by a nearby arginine at the membrane–enzyme interface. In addition, the structure provides a model for how the v-end of the lipophilic co-substrate is pinned at one end of a hydrophobic cleft, providing a molecular ‘ruler’ to align the eactive epoxide at the thiol of glutathione. This provides new structural insights nto the mechanism of LTC4 formation, and also suggests that the observed inding and activation of GSH might be common for a family of homologous proteins mportant for inflammatory and detoxification responses.
|
|
| 5. |
- Andersson, Magnus, et al.
(författare)
-
A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins
- 2008
-
Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 16:1, s. 21-28
-
Tidskriftsartikel (refereegranskat)abstract
- Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.
|
|
| 6. |
|
|
| 7. |
- Nachin, Laurence, 1971, et al.
(författare)
-
Heterodimer formation within universal stress protein classes revealed by an in silico and experimental approach.
- 2008
-
Ingår i: Journal of molecular biology. - : Elsevier BV. - 1089-8638 .- 0022-2836. ; 380:2, s. 340-50
-
Tidskriftsartikel (refereegranskat)abstract
- Universal stress proteins (Usps) are found in all kingdoms of life and can be divided into four classes by phylogenic analysis. According to available structures, Usps exist as homodimers, and genetic studies show that their cellular assignments are extensive, including functions relating to stress resistance, carbon metabolism, cellular adhesion, motility, and bacterial virulence. We approached the question of how Usps can achieve such a variety of functions in a cell by using a new procedure for statistical analysis of multiple sequence alignments, based on physicochemically related values for each amino acid residue of Usp dimer interfaces. The results predicted that Usp proteins within a class may, in addition to forming homodimers, be able to form heterodimers. Using Escherichia coli Usps as model proteins, we confirmed the existence of such interactions. We especially focused on class I UspA and UspC and demonstrated that they are able to form homo- and heterodimers in vitro and in vivo. We suggest that this ability to form both homo- and heterodimers may allow for an expansion of the functional repertoire of Usps and explains why organisms usually contain multiple usp paralogues.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
|
|
