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1

3D domain swapping ? implications for conformational disorders and ways of control

100%
Jaskolski M.
Biotechnologia
|
2011
|
issue 1
34-44
EN
3D Domain swapping is a mechanism of protein aggregation, in which a structural element of a protein fold is replaced by an identical element from another subunit. Some proteins, for instance RNase A, can assume many domain- swapped forms, thus undermining the dogma,'one sequence ? one structure' in a particularly spectacular way. Completed in a mutual fashion, it is a mechanism of protein oligomerization. In an open-ended fashion, 3D domain swapping could be a mechanism of amyloid fibril formation. In another mechanism, possibly operating together with domain swapping, a specific sequence, such as a glutamine expansion, could form a ?-spine of the fibril in a motif called steric zipper. The first connection between 3D domain swapping and amyloidogenicity was established in human cystatin C (HCC), the second - in the prion protein (PrP). In both cases, a disulfide bridge (natural in PrP, engineered in HCC) can be used for redox control of 3D domain swapping and to demonstrate that it is indeed involved in amyloid fibril formation. HCC has a naturally occurring L68Q mutant with drastically increased propensity for aggregation. The L68Q mutation occurs at the closed interface, or protein core. Mutations in other areas, such as the flexible hinge (especially deletions and insertions) can also be used to control 3D domain swapping and aggregation. Paradoxically, 3D domain swapping can also be used by Nature for prevention of nucleation processes that lead to high-order aggregates or crystals. Such a situation exists in the eye lens, where despite astronomical concentration of crystallins, the solution remains clear. One of the Nature's tricks to achieve polydispersity is to use a palindromic sequence for the swapped domain, thereby frustrating the growth of aggregates by constantly changing the interaction topology.
2
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From Atomic Resolution to Molecular Giants: an Overview οf Crystallographic Studies of Biological Macromolecules with Synchrotron Radiation

100%
Jaskolski M.
|
|
issue 2
257-263
EN
Protein crystals have huge unit cells ( ≈100 Å) filled not only with ordered protein molecules but also in about 50% with liquid water. The phase problem in protein crystallography can be solved by molecular replacement (using a suitable model molecule), by isomorphous replacement (using heavy atom derivatives), or by multiwavelength anomalous difraction (using resonant scattering of synchrotron-generated X-rays by anomalous atoms, such as Se). X-ray diffraction by protein crystals produces thousands of reflections but since the models are very complex (many thousands of atoms), paucity of data is a serious problem and stereochemical restraints are necessary. In consequence, the highest possible resolution (minimum d-spacing in Bragg's Equation) should always be the experimental goal. Protein structures determined by crystallography are deposited in protein data bank, which currently holds more than 62000 entries. Recent methodological advancements, stimulated by a wide-spread use of powerful synchrotron sources and by structural genomics, have resulted in rapid acceleration of the structure elucidation process, and in addition help to obtain a better data. Protein crystallography has produced atomic models of gigantic macromolecular assemblies, including the ribosome. It is also providing accurate targets for structure-guided development of drugs.
3
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Prion Diseases: a dual view of the prion hypothesis as seen from a distance

63%
Liberski P. P., Jaskolski M.
Acta Neurobiologiae Experimentalis
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2002
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vol. 62
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issue 3
197-226
EN
We review the historical background and principles of the prion theory in its current shape. We showed that most of data may be still interpreted dually according to the protein only hypothesis and according to the theory in which additional component is necessary to comprise the infectivity. The enormous impact of structural biological studies is also stressed.
4

Reverse transcriptase as the enzyme responsible for the genetic variability of human immunodeficiency virus (HIV)

51%
Kurzynska-Kokorniak A., Jaskolski M., Figlerowicz M.
Biotechnologia
|
2002
|
issue 1
24-34
EN
Human immunodeficiency virus (HIV), the causative agent of AIDS, belongs to the particularly dangerous and, as a result, the most extensively studied viruses. Until now no effective method protecting against this pathogen has been developed. The major problem is the unusual genetic diversity of HIV, which helps the virus to escape from immunological response and to produce drug-resistant mutants. Most of the collected data suggest that HIV-encoded reverse transcriptase (HIV RT) is the main factor responsible for the continuos generation of new viral variants. There are two primary mechanisms involved in the generation of HIV mutants: high error prone replication and genetic RNA recombination. In this article both processes are discussed in detail.
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