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- Almstedt, Karin, 1980-, et al.
(författare)
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Unfolding a folding disease: folding, misfolding and aggregation of the marble brain syndrome-associated mutant H107Y of human carbonic anhydrase II
- 2004
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Ingår i: Journal of Molecular Biology. - Oxford : Elsevier. - 0022-2836 .- 1089-8638. ; 342:2, s. 619-633
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Tidskriftsartikel (refereegranskat)abstract
- Most loss-of-function diseases are caused by aberrant folding of important proteins. These proteins often misfold due to mutations. The disease marble brain syndrome (MBS), known also as carbonic anhydrase II deficiency syndrome (CADS), can manifest in carriers of point mutations in the human carbonic anhydrase II (HCA II) gene. One mutation associated with MBS entails the His107Tyr substitution. Here, we demonstrate that this mutation is a remarkably destabilizing folding mutation. The loss-of-function is clearly a folding defect, since the mutant shows 64% of CO2 hydration activity compared to that of the wild-type at low temperature where the mutant is folded. On the contrary, its stability towards thermal and guanidine hydrochloride (GuHCl) denaturation is highly compromised. Using activity assays, CD, fluorescence, NMR, cross-linking, aggregation measurements and molecular modeling, we have mapped the properties of this remarkable mutant. Loss of enzymatic activity had a midpoint temperature of denaturation (Tm) of 16 °C for the mutant compared to 55 °C for the wild-type protein. GuHCl-denaturation (at 4 °C) showed that the native state of the mutant was destabilized by 9.2 kcal/mol. The mutant unfolds through at least two equilibrium intermediates; one novel intermediate that we have termed the molten globule light state and, after further denaturation, the classical molten globule state is populated. Under physiological conditions (neutral pH; 37 °C), the His107Tyr mutant will populate the molten globule light state, likely due to novel interactions between Tyr107 and the surroundings of the critical residue Ser29 that destabilize the native conformation. This intermediate binds the hydrophobic dye 8-anilino-1-naphthalene sulfonic acid (ANS) but not as strong as the molten globule state, and near-UV CD reveals the presence of significant tertiary structure. Notably, this intermediate is not as prone to aggregation as the classical molten globule. As a proof of concept for an intervention strategy with small molecules, we showed that binding of the CA inhibitor acetazolamide increases the stability of the native state of the mutant by 2.9 kcal/mol in accordance with its strong affinity. Acetazolamide shifts the Tm to 34 °C that protects from misfolding and will enable a substantial fraction of the enzyme pool to survive physiological conditions.
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| 2. |
- Thorgeirsson, Thorgeir E, et al.
(författare)
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A variant associated with nicotine dependence, lung cancer and peripheral arterial disease
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7187, s. 9-638
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Tidskriftsartikel (refereegranskat)abstract
- Smoking is a leading cause of preventable death, causing about 5 million premature deaths worldwide each year(1,2). Evidence for genetic influence on smoking behaviour and nicotine dependence (ND)(3-8) has prompted a search for susceptibility genes. Furthermore, assessing the impact of sequence variants on smoking-related diseases is important to public health(9,10). Smoking is the major risk factor for lung cancer (LC)(11-14) and is one of the main risk factors for peripheral arterial disease (PAD)(15-17). Here we identify a common variant in the nicotinic acetylcholine receptor gene cluster on chromosome 15q24 with an effect on smoking quantity, ND and the risk of two smoking- related diseases in populations of European descent. The variant has an effect on the number of cigarettes smoked per day in our sample of smokers. The same variant was associated with ND in a previous genomewide association study that used low- quantity smokers as controls(18,19), and with a similar approach we observe a highly significant association with ND. A comparison of cases of LC and PAD with population controls each showed that the variant confers risk of LC and PAD. The findings provide a case study of a gene - environment interaction(20), highlighting the role of nicotine addiction in the pathology of other serious diseases.
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| 3. |
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| 4. |
- Abdulla, Parosh Aziz, et al.
(författare)
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Algorithmic Improvements in Regular Model Checking
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Regular model checking is a form of symbolic model checking for parameterized and infinite-state systems, whose states can be represented as finite strings of arbitrary length over a finite alphabet, in which regular sets of words are used to represent sets of states. In earlier papers, we have developed methods for computing the transitive closure (or the set of reachable states) of the transition relation, represented by a regular length-preserving transducer. In this paper, we present several improvements of these techniques, which reduce the size of intermediate approximations of the transitive closure: One improvement is to pre-process the transducer by \em bi-determinization, another is to use a more powerful equivalence relation for identifying histories (columns) of states in the transitive closure. We also present a simplified theoretical framework for showing soundness of the optimization, which is based on commuting simulations. The techniques have been implemented, and we report the speedups obtained from the respective optimizations.
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| 5. |
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| 6. |
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| 7. |
- Abdulla, Parosh Aziz, et al.
(författare)
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Regular Model Checking for LTL(MSO)
- 2004
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Ingår i: Proc. 16th Int. Conf. on Computer Aided Verification, LNCS.
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Tidskriftsartikel (refereegranskat)
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| 8. |
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| 9. |
- Abdulla, Parosh Aziz, et al.
(författare)
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Regular Tree Model Checking
- 2002
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Ingår i: CAV 2002, 14th Int. Conf. on Computer Aided Verification.. ; , s. 555-568
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Konferensbidrag (refereegranskat)
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| 10. |
- Abdulla, Parosh, et al.
(författare)
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A Survey of Regular Model Checking.
- 2004
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Ingår i: CONCUR 2004 - Concurrency Theory. - 354022940X ; , s. 35-48
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Konferensbidrag (refereegranskat)abstract
- Regular model checking is being developed for algorithmic verification of several classes of infinite-state systems whose configurations can be modeled as words over a finite alphabet. Examples include parameterized systems consisting of an arbitrary number of homogeneous finite-state processes connected in a linear or ring-formed topology, and systems that operate on queues, stacks, integers, and other linear data structures. The main idea is to use regular languages as the representation of sets of configurations, and finite-state transducers to describe transition relations. In general, the verification problems considered are all undecidable, so the work has consisted in developing semi-algorithms, and decidability results for restricted cases. This paper provides a survey of the work that has been performed so far, and some of its applications.
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