this binding requires.
CˆAMARA, A. S.1; HORJALES REBOREDO, E.1 [email protected]
1Instituto de F´ısica de S˜ao Carlos - USP
The complexity of a living organism is not proportional to its number of genes. In fact, “natural selection operates on phenotypes rather than genotype” (1), and the more easily an organism adapts to the changes in physiological and environmental conditions, the more chances it has to survive and reproduce.
Therefore, some mechanisms exist to ensure proper and sensitive genetic expression. Transcriptional regulation is one of them. And due to its combinatorial nature, it enhances regulatory complexity, diversity and physiological and behavioural complexity. (2) This combinatorial nature means that macro and micro biomolecules may gather in countless ways to form an unique structure that specifically binds to a DNA site. This binding depends not only on recognizing a base sequence, but also on adopting a conformation that is compatible with the geometry and charge distribution of the DNA double helix. We analyse here some simple and homodimeric transcriptional regulators (TR), which present a very common motif, the helix-turn-helix (HTH). This motif interacts with the DNA both specifically and non-specifically, and in a homodimer, where it appears twice in the same biological unit, they are symmetrically placed in a way that two helices fit exactly into two consecutive major grooves of the DNA. These proteins are also allosterically regulated, which means the DNA-binding site goes through large conformational changes upon the binding of a different ligand on a distant site. This is a simple example of the combinatorial nature of the transcriptional regulation. Alone a TR has very low probability of binding to DNA, but if another ligand, macro or micro, binds to its allosteric site, this probability is changed and binding is enhanced by the conformational changes. Thus, we focused on identifying structural and conformational characteristics of some TR complexed to DNA, which structures are present on the Protein Data Bank. We analyse characteristics such as: distance and orientation between the recognition helices; the arrangement of residues in these helices; the bases they interact with; the extent of the DNA site; an the presence of palindromic sequences. With these informations, it maybe possible to predict the conformation of the DNA-binding motif of a TR while complexed to DNA, if only its apo conformation and its DNA-site sequence are known. And therefore, we propose a model for a TR structure our group has recently resolved, calculated as a linear combination of harmonic modes simulated for this protein in the apo conformation. These harmonic modes of low frequency, which collectively moves large groups of atoms, are likely to represent functional motions of the protein (3), and also the allosteric transition that occurs upon the binding of the allosteric ligand. By identifying the motion required to change the conformation of the DNA-binding motif, we also identify modifications in the allosteric site, and thus we can also predict stereo-chemical characteristics of an allosteric ligand still unknown. If a ligand with these characteristics is experimentally confirmed to bind to this TR, this maybe a novel procedure to predict drugs that affect transcriptional regulation.
Referˆencias:
1 JAROSZ, D. F.; TAIPALE, M.; LINDQUIST, S. Protein homeostasis and the phenotypic manifestation of genetic diversity: principles and mechanisms. Annual Review of Genetics, v. 44, p. 189-216, 2010.
doi: 10.1146/annurev.genet.40.110405.090412.
2 LEVINE, M.; TIJAN, R. Transcription regulation and animal diversity. Nature, v. 424, n. 6945, p.
147-151, 2003.
3 ANSARI, A. et al . Protein states and proteinquakes. Proceedings of the National Academy of Sciences of the United States of America , v. 82, n. 15, p. 5000-5004, 1985.
PG41
Simula¸ c˜ oes ambientais e caracteriza¸ c˜ ao espectrosc´ opica in-situ de potenciais bioassinaturas moleculares para aplica¸ c˜ ao em miss˜ oes espaciais
CERINI, M. F.1; RIVAS, N.1; GALANTE, D.1 [email protected]
1Laborat´orio Nacional de Luz S´ıncrotron - LNLS
O presente projeto tem como objetivo a investiga¸c˜ao em laborat´orio da fotoestabilidade e resiliˆencia de biomol´eculas em ambientes extraterrestres simulados, usando m´etodos espectrosc´opicos. Os resultados ser˜ao utilizados para melhor definir as condi¸c˜oes de detectabilidade de bioassinaturas espectrosc´opicas, com aplica¸c˜oes para o desenvolvimento de experimentos de astrobiologia em miss˜oes espaciais de pequeno porte e baixo custo. Tais miss˜oes est˜ao em andamento pelo grupo de pesquisa no qual o projeto est´a inserido, que incluem bal˜oes estratosf´ericos e CubeSats. Biomol´eculas de importˆancia astrobiol´ogica ser˜ao selecionadas entre diversas classes, como amino´acidos, pigmentos biol´ogicos, bases nucleot´ıdicas, porfirinas, Hidrocarbonetos Polic´ıclicos Arom´aticos (PAH) e outras, e ser˜ao submetidas a diferentes ambientes simulados (especialmente a superf´ıcie de Marte e o ambiente espacial). Os experimentos ser˜ao realizados nas instala¸c˜oes do Laborat´orio Nacional de Luz S´ıncrotron (LNLS), em especial na linha de luz TGM (Toroidal Grating Monochromator). Essa esta¸c˜ao experimental trabalha na regi˜ao de raios X mole e ultravioleta de v´acuo (3 a 330 eV), e ser´a utilizada para simular as condi¸c˜oes do ambiente espacial, medindo mudan¸cas f´ısicas e qu´ımicas nas biomol´eculas expostas por reflectˆancia no UV-Vis in-situ e em fun¸c˜ao do tempo. Ser´a tamb´em utilizada a Cˆamara de Simula¸c˜ao Espacial e Planet´aria (AstroCam) do N´ucleo de Pesquisa em Astrobiologia da USP (NAP/Astrobio) (1), com a qual outros parˆametros ambientais tamb´em poder˜ao ser controlados, como radia¸c˜ao, press˜ao, composi¸c˜ao gasosa e temperatura. As mudan¸cas nas biomol´eculas s˜ao medidas in-situ por an´alises espectrosc´opicas e outros m´etodos convencionais de laborat´orio.
Palavras-chave: Bioassinaturas. Astrobiologia. Simula¸c˜oes ambientais.
Referˆencias:
1 UNIVERSIDADE DE S˜AO PAULO. Instituto de Astronomia, Geof´ısica e Ciˆencias Atmosf´ericas. N´ucleo de Pesquisa em Astrobiologia. Astrobiologia. Dispon´ıvel em: <http://www.astrobiobrazil.
org/>. Acesso em: 23 ago. 2016.