Systems Biology • Structural Biology Dr. Shaila C. Rössle 1
Our life is maintained by molecular network systems Our life is maintained by molecular network systems Molecular network system in a cell (From ExPASy Biochemical Pathways; http://www.expasy.org/cgi-bin/show_thumbnails.pl?2
Systems Biology Hiroaki Kitano, Science 2010
Glutamate Metabolism KEGG
2.4.2.1 2.7.1.59 4 6.3.5. 2.3.1.4 2.6.1.16 1 6.1.1.18 6.3.5.2 6.3.5.5 6.3.5.7 2.7.2. 6.3.5.5 2 3.5.1.3 6.3.1.2 3.5.1.38 5.1.1.3 6.1.1.17 1.4.1.13 1.5.1.12 2.6.1. 2.6.1.1 1.4.1.3 2 1.2.1.24 6.3.2.2 1.8.1.7 6.3.2.3 6.1.1.17 4.1.1.15 2.6.1.19
Proteins 6
Proteins Proteins have a variety of roles that they must fulfil: • They are the enzymes that rearrange chemical bonds • They carry signals to and from the outside of the cell, and within the cell • They transport small molecules • They form many of the cellular structures • They regulate cell processes, turning them on and off and controlling their reates
Proteins play key roles in a living system Proteins play key roles in a living system • Three examples of protein functions Alcohol dehydrogenas – Catalysis: e oxidizes alcohols to Almost all chemical reactions in a aldehydes or living cell are catalyzed by protein ketones enzymes. – Transport: Some proteins transports various Haemoglobin carries substances, such as oxygen, ions, oxygen and so on. – Information transfer: For example, hormones. Insulin controls the amount of sugar in the blood
Proteins A protein is a polymer of a fixed length, composition and structure made by a combination of the 20 naturally occurring amino acids.
Amino acid: Basic unit of protein Amino acid: Basic unit of protein R Different side + C chains, R, NH 3 COO - determin the Amino group Carboxylic properties of 20 acid group H amino acids. An amino acid
Proteins – amino acids • There are 20 different types of amino acids • Different sequences of amino acids fold into different 3D shapes • Proteins can range from fewer than 20 to more than 5000 amino acids in length • Each protein that an organism can produce is encoded in a piece of the DNA called a “gene“ • The single-celled bacterium E.coli has about 4300 different genes • Humans are believed to have about 30,000 different genes
Charged amino acids Special cases Polar but uncharged hydrophobic 12
From the book: “DNA: The Secret of Life” by James 13 Watson and Andrew Berry
Translation - detail UAA 3’ 5’ mRNA C AUG AUG RIBOSOME N N N N Termination Initiation Elongation In Prokaryotes : A special sequence (Shine- The starting sequence AUG codes for Dalgarno) identifies the starting AUG. Methionine and is present several times (Multiple proteins on the same mRNA). in the mRNA sequence. In Eukaryotes : It is the first AUG sequence starting from the 5’ terminus. (Only one protein for each mRNA).
Proteins • Proteins are key players in our living systems. • Each protein folds into a unique three-dimensional structure defined by its amino acid sequence.. • Protein structure is closely related to its function. • Protein structure prediction is a grand challenge of computational biology.
Protein Structure
The levels of protein structure Molten globule
Each Protein has a unique structure Each Protein has a unique structure Amino acid sequence NLKTEWPELVGKSV EEAKKVILQDKPEAQ IIVLPVGTIVTMEYRI DRVRLFVDKLDNIAE VPRVG Foldin g!
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PSI Omega PHI Ligação Peptídica
he levels of protein structure Molten globule
Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns. 22
Supersecondary structure Supersecondary structure α-helix β-sheet
Ramachandran plot 24
Loops and Turns - Conectam elementos de estrutura secundária. Hairpin loops: conectam duas folhas betas antiparalelas (formam os sítios de ligação de anticorpos). - Vários tamanhos e formas irregulares - Estão na superfície da proteína (ricos em resíduos polares e carregados) - Freqüentemente participam na formação de sítios de ligação e sítios ativos de enzimas - Problema importante de modelagem (possuem estruturas preferenciais).
The levels of protein structure Molten globule
Tertiary structure 27
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Protein domains Pairwise sequence comparison of proteins led to strange results • A domain is an independent folding unit • A domain is the next step up in complexity from a motif • There appear to be a limited number of folds (domains) that can be made from the 20 natural aa’s • Domain unit of evolution • Mixing and matching can create new function and regulation • Most proteins involved in cell signalling consist exclusively of small domains interspersed by linker regions.
Database of protein domains – Search tools • Prosite - expasy.org/prosite/ • Smart - smart.embl-heidelberg.de • ProDom - prodom.prabi.fr/ • InterPro -www.ebi.ac.uk/interpro/ • Pfam - pfam.sanger.ac.uk/ 30
Tertiary structure. DNA-binding proteins. Cys Cys Zn Cys Cys The zinc finger
Disordered Regions ot all proteins are structured: Intrinsically Unstructured Proteins Proteins (segments of proteins) that are lacking well- structured 3-dimentional fold. They are referred as “natively denatured/unfolded”, “intrinsically unstructured/unfolded”. About 35-51% of the proteins have unstructured regions that are longer than 50 residues; 6-17% of proteins in the Swiss-Prot are probably fully disordered. Determined by neural networks predictors (based on the protein sequence).
Coupling of folding to target binding KID domain of CREB pKID bound to KIX domain of CBP (CREB binding protein). • Can provide tighter binding than similar sized, folded prote • Enthalpy-Entropy compensation. • Allows post-translational modification. Predicted α -helices in free peptide Experimentally determined α -helices in complex
Unstructured proteins can adopt multiple structures upon target binding- they are “plastic” Hif1 α peptide bound to the TAZ1 domain of the Creb binding protein. Here the peptide forms an α -helix. Hif1 α peptide bound to asparagine hydroxylase. Here the peptide binds in an extended conformation.
he levels of protein structure Molten globule
Quaternary structures. Transport protein K+ channel Enzyme - HIV-1 protease Haemoglobin
Peptidase
A few examples of common structural motifs H H T Helix-turn-Helix: a basic nucleic acid binding structure. This motif (green on left) and the exact relationship between the helices is conserved from bacteria to man.
Structural Classification of Proteins • SCOP • CATH 39
Close relationship between protein structure and its Close relationship between protein structure and its function function Example of enzyme Hormone receptor Antibody reaction substrate s A enzym enzym e e B Matching Digestion the shape of A! to A enzym e A Binding to A
Molecular Interaction types • Internal • Domain-domain • Homo-obligomer • Homo-oligomer • Hetero-oligomer HIV gp120 / CD4 / FAB PD Kwong, R Wyatt, J Robinson, RW Sweet, J Sodroski & WA Hendrickson (1998) Nature 393, 648-659.PD Kwong, R Wyatt, S Majeed, J Robinson, RW Sweet, J Sodroski & WA Hendrickson (2000) Structure 8, 1329-1339. 41
How Proteins interact The Cell 42
Interactions forces 43
Example - van der Waals force A molecule contains a cavity exactly complementary in shape to a protruding group of another molecule 44
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Wikipedia 46
• Inhibitor for anti-apoptotic protein In a leucine zipper DNA-binding protein the two helices are held together by hydrophobic interactions between, mainly, leucine sidechains 47
The Cell 48
responsible for DNA binding according to Duval et al (2002) 49
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Glaser et al. (2003) Bioinformatics 19:163-164 51
Some 4 helix bundle proteins Cytokines: secreted proteins that regulate cellular function.
The β -barrel OmpF porin is a non-specific transport channel that allows for the passive diffusion of small, polar molecules (600-700 Da in size) through the cell's outer membrane. Such molecules include water, ions, glucose, and other nutrients as well as waste products (Cowan et al., 1995).
Analyzing Protein Structure and Function • Methods currently used to characterize protein structure and function • Techniques used to determine the three-dimensional structure of proteins • Methods that are used to predict how a protein functions, based on its homology to other known protein • Methods to predict its location inside the cell • Techniques for detecting protein-protein interactions 54
Methods currently used to characterize protein structure and function • Site-directed mutagenesis • Nuclear magnetic resonance • Mass spectrometry • Proteomics (2D eletrophoresis) • Protein microarrays 55
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