Homology inference with specific molecular constraints

Evolutionary processes can be considered at multiple levels of biological organization. The work developed in this thesis focuses on protein molecular evolution. Although proteins are linear polymers composed from a basic set of 20 amino acids, they generate an enormous variety of form and function. Proteins that have arisen by a common descent are classified into families; they often share common properties including similarities in sequence, structure, and function. Multiple methods have been developed to infer evolutionary relationships between proteins and classify them into families. Yet, those generic methods are often inaccurate, especially when specific protein properties limit their applications. In this thesis, we analyse two protein classes that are often difficult for the evolutionary analysis: the coiled-coils – repetitive protein domains defined by a simple widespread peptide motif (chapters 2 and 3) and Rab small GTPases – a large family of closely related proteins (chapters 4 and 5). In both cases, we analyse the specific properties that determine protein structure and function and use them to improve their evolutionary inference

Squalamine in the interfacial region of the lipid bilayer built of lipid A

Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria. Lipid A is a part of LPS which anchors LPS in the bilayer. The integrity of the membrane is crucial for survival of each living cell. Therefore, the compounds which possess the ability to destroy the integrity, so called membrane active compounds, are promising antimicrobial drugs. Squalamine an aminosterol antibiotic derived from the shark is a membrane active compound. Experimental data demonstrates that squalamine kills Gram-negative bacteria by membrane disruption. However, the detailed molecular mechanism is still unknown. In this work we described at the atomic resolution an initial stage of interactions between squalamine and the model lipid bilayer composed of lipid A. Data presented in this thesis indicate that squalamine strongly interacts with lipid A headgroups by hydrogen bonds and water bridges. Despite no hydrophobic interactions were found, the noticeable influence of squalamine on the membrane core occurs. Moreover, presented evidence demonstrates that squalamine orientation within membrane/water interface is determined and a conformational dynamics of the molecule depends on interaction with lipid A.Podstawowym składnikiem zewnętrznej warstwy zewnętrznej błony bakterii Gram-ujemnych jest lipid A, stanowiący kotwicę lipidową lipopolisacharydu. Integralność błony komórkowej jest niezbędna do przeżycia każdej komórki. Niektóre związki, tzw. związki błonowo czynne, wykazują zdolność selektywnego zaburzania błony w stopniu zależnym od jej składu lipidowego. Jednym z takich związków jest skwalamina, aminosterol pochodzenia naturalnego, która charakteryzuje się zdolnością specyficznego oddziaływania z lipidami tworzącymi błony bakteryjne. Dane eksperymentalne wskazują, że skwalamina wykazuje działanie bakteriobójcze na drodze rozrywania błony bakteryjnej. Molekularne podstawy tego procesu nie są jednak znane. W niniejszej pracy opisano z rozdzielczością atomową początkowe oddziaływania między skwalaminą a modelem zewnętrznej błony bakteryjnej. Analiza trajektorii przeprowadzonej symulacji dynamiki molekularnej modelowej dwuwarstwy złożonej z lipidu A i skwalaminy wykazały, że skwalamina oddziałuje z polarnymi głowami lipidowymi, tworząc wiązania wodorowe i pomosty wodne. Skwalamina wpływa również silnie na strukturę hydrofobowego wnętrza błony pomimo braku oddziaływań niepolarnych z łańcuchami węglowodorowymi lipidu A. Przeprowadzone analizy wskazują, że skwalamina przyjmuje preferowane orientacje w obrębie błony, a dynamika zmian konformacyjnych w cząsteczce jest zależna od oddziaływania z lipidami

Czy zamienne stosowanie klasyfikacji zaawansowania nowotworów endometrium według Międzynarodowej Federacji Ginekologów i Położników z 1988 roku i z 2009 roku może prowadzić do istotnych pomyłek klinicznych?

Introduction: Since 2009 the new FIGO Staging System of endometrial cancer, which changed the previousFIGO 1988 Staging System, has been present. Unfortunately, parallel use of both classifications is observed.Aim of study: to assess whether parallel use of the 2009 and the 1988 FIGO staging systems can causesignificant therapeutic mistakes in patients with endometrioid endometrial cancer.Material and methods: We analysed 262 patients with endometrioid endometrial cancer. The endometrialcancers were staged in both classifications. We analysed possible therapeutic mistakes caused by diverse nomenclature.Results: The patients at low risk, intermediate risk, and high risk for relapse were presented in: 110 (41.6%),109 (42.0%) and 43 (16.4%) cases, respectively. The possibility of inappropriate qualification for adjuvant treatmentoccurred in 102 patients (38.9%) if they were staged in the FIGO 1988 classification and interpreted as theFIGO 2009 classification, and similarly, in 65 patients (24.8%) if they were staged in the FIGO 2009 classificationand interpreted as the FIGO 1988 classification. The risk of a decision mistake in terms of the adjuvant treatmentdue to diverse nomenclature was observed commonly in 167 patients (63.7%).Conclusions: The common use of both FIGO staging systems for endometrioid endometrial cancer cancause significant therapeutic mistakes in terms of the adjuvant treatment. There is a need to use only the newFIGO 2009 Staging System for endometrial cancer and stop using the FIGO 1988 Staging System to avoid therapeuticmistakes