5- dna protein interactions 2014

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Fuerzas que participan en las interacciones DNA-Proteína EXPRESION GENICA o el Flujo de Información horizontal Jorge Arevalo 2014

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  • Fuerzas que participan en las interacciones DNA-Protena

    EXPRESION GENICA o el Flujo de Informacin horizontal

    Jorge Arevalo 2014

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.7 Genes of tryptophan operon of E. coli. Described in Yanofsky, C. Trends in Genet. 20: 367, 2004.

  • Protein-DNA interactions

    usually involve some degree of sequence specificity

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.21 The TATA-binding protein (TBP) has been cocrystallized with DNA. Figure reproduced with permission from Voet, D., Voet, J., and Pra?, C. W. Fundamentals of Biochemistry. New York: Wiley, 1999. (1999) John Wiley & Sons, Inc.

  • Structural information is now available on over 400 distinct DNA-protein complexes, from a wide range of eukaryotic and prokaryotic sources. Studies of the proteins themselves rarely provide sufficient insight into the processes of recognition. The determination of the human genome sequence in 2001 has enabled reliable estimates to be made for the numbers of genes with particular functions. Of the 30000 in total, 13.5 per cent (2308) are proposed to be involved in nucleic acid binding, of which 6 per cent (1850) are estimated to be transcription factors.

  • Non-specific binding

    Electrostatic forces are long range and not very specific. They rule the attraction between the positively charges protein surface (all DNA-binding domains have exposed basic side chains) and the negatively charged DNA phosphate backbone. Once protein and DNA are nearby due to electrostatic interactions, the other forces, which are shorter-range, become effective. These, and predominantly hydrogen bonds between amino acid side chains and nucleic acid bases, determine the protein-DNA binding specificity.

  • Once protein and DNA are nearby due to electrostatic interactions, the other forces, which are shorter-range, become effective. These, and predominantly hydrogen bonds between amino acid side chains and nucleic acid bases, determine the protein-DNA binding specificity.

  • Specific binding (universal amino acid-base interactions)

    The only regions where the bases are available for interaction are at the floor of the grooves. These are paved with nitrogen and oxygen atoms that can make hydrogen bonds with the side chains of a protein.

  • 1. Hydrogen bonds

    Possible binding sides of DNA base pairs

  • Donadores ( +) y Aceptores de puentes de hidrgeno( ). Existen posiciones que no forman puentes de hidrgeno pero pueden participar de interacciones electrostticas ( )

  • The B-DNA major groove is the richer of the two groove of the duplex DNA, both in information content per se, and in its ability to facilitate discrimination between DNA sequences, which is essential if the appropriate genes are to be transcribed. Thus, the major groove is generally the site of direct information readout. Nonetheless, the minor groove is an important target for some regulatory and structural proteins, especially those that able to deform DNA so that the minor groove becomes greatly expanded.

  • For GC pair, the major groove exposes a hydrogen-bond acceptor, G N7, another acceptor, G O6, a hydrogen-bond donor, C NH4, and finally, a hydrogen atom at C5. The minor groove displays a hydrogen-bond acceptor G N3, a donor G NH2 and an acceptor C O2.

  • For the AT pair, the major groove gives the following sequence : an acceptor A N7, donor A NH6, acceptor T O4, and a methyl group at T5. The minor groove displays an acceptor, a hydrogen atom and a donor. These patterns for potential hydrogen bonds are clearly quite different for the different base pairs in the major groove, and they could easily be recognized and distinguished by a protein molecule.

  • Clearly, the major groove is a much better candidate for sequence-specific recognition than the minor groove for two reasons. First, the major groove is wider than the minor, and the bases are thus more accessible to a protein molecule. Second, the pattern of possible hydrogen bonds from the edges of the base pairs to a protein are more specific and discriminatory in the major groove than in the minor.

    Only a rather limited number of base pairs is needed to provide unique and discriminatory recognition sites in the major groove.

  • The above figure gives the color codes for the hexanucleotide recognition sites of three different restriction enzymes - Eco RI, Bal I and Sma I. It is clear that these patterns are quite different, and each can be uniquely recognized by specific protein-DNA interactions.

  • Puentes de hidrgeno de Arg, Gln y Aspn

  • There is no general 1:1 amino acid : DNA base correspondence, and recognition can sometimes occur in a wide variety.

    Here the distribution of amino acid-base interactions in 129 protein-DNA Structures (Luscombe et., 2001) : Gua Cyt Ade Thy #sum ----------------------------------------------------------------------------------- Arginine (R) 98 8 19 24 149 Lysine (K) 30 6 4 9 49 Serine (S) 12 2 1 3 18 Asparagine (N) 7 10 18 7 42 Glutamine (Q) 6 2 16 2 26 Glutamate (E) 1 10 1 0 12

    #sum 154 38 59 45 296 The majority of interactions involve O6 and/or N7 atoms of guanine bases forming hydrogen bonds with the charged ends of long flexible side chains from the basic residues arginine or lysine, the amide residues glutamine and Asparagine or the hydroxyl group of a serine.

  • Arg Gua : a perfect H-bonding association (33% of the total of amino acid-base pair interactions)

    DNA-binding domain of Tc3 transposase from C elegans residue : Arg C236

    PDBcode: 1tc3 R = 2.45 R-factor = 0.234

    1.82 1.96

    2 H-bond acceptors

    2 H-bond donors

    guanidinium moeity

  • Asn/Gln Ade : another frequent H-bonding association (11% of the total of amino acid-base pair interactions)

    formamide group

    one H-bond acceptors

    one H-bond donors

    one H-bond donors

    one H-bond acceptors

    Pit-1 Pou domain residue : Asn A44 PDBcode : 1au7 R = 2.30 R-factor = 0.230

    2.13

    1.96

  • Recently, Cheng et al. (2003) have calculated all geometrically plausible H-bonding arrangements between amino acid and nucleic acid base (DNA and RNA recognition). They have found 32 possible interactions, with 17 of which have been observed in complex structures. (The number of observed Cases are indicated here in red).

    2

    18 84

    5

    1

    2

    6

    183 26

    3 10

    1

    5

    2

    3

    25 7

  • PDBcode: 1tc3 R = 2.45 R-factor = 0.234

    DNA-binding domain of Tc3 transposase from C elegans residues : Arg C236-A7-A8

    Cation-/H-bond stair motif involve two nucleobases and an amino acid side chain. Its encompass three different types of interactions : - stacking, H-bond and cation- interactions.

  • Zinc finger protein PDBcode : 1mey R = 2.20 R-factor = 0.224

    Methyltransferase PDBcode : 6mht R = 2.05 R-factor = 0.186

    Sap-1 ets domain PDBcode : 1bc8 R = 1.93 R-factor = 0.220

    Homeodomain From drosophila PDBcode : 1fjl R = 2.00 R-factor = 0.198

  • Protein can bind the DNA through the base, sugar, and the phosphate group

    Hydrogen bonds with phosphate are not specific, but with great importance in stabilizing the protein-DNA complexes

    Guanine exposes the greatest number of potential hydrogen-bonding atoms on the base edge(4 positions)

    The polar and charged residues of amino acids play a central role

    Arg > Lys > Ser > Thr; Asn and Gln Acidic residues are used sparingly Asp and Glu Only Gly makes a significant number of interaction Few interactions are produced by hydrophobic residues

  • Favored amino acid-base hydrogen bonds

    Arg and Lys --- G, Asp and Glu --- A, Ser and His --- G 80% of Ser and Thrs interactions are with the DNA

    backbone

    Hydrogen bond geometries Single 36.9% Bidentate 33.8% ( two or more hydrogen bonds are

    made with a base or base pair) Complex 34.1% ( a protein residue binds more than

    one step simultaneously)

  • Example: Bidentate interaction with Arg

  • 2. Van der waals contacts

    Comprise 64.9% of all protein-DNA interactions

    Interactions with the DNA backbone ( sugar and phosphate) are most prominent

    Interactions with the phosphate group dominate due to their high exposure on the DNA surface

    T>A>G>C Arg, Thr, Phe, Ile, His, Cys

  • Phe and His may have ring stacking interactions with the base ring

    Cys in coordinating proteins has a high propensity to contact the DNA backbone

    Glu, Ala, Leu, and Asp are less favored: Glu and Asp: electrostatic interactions with

    DNA Ala and Leu: shortness of their side chains

  • 3. Water mediated bonds

    Nearly as common as direct hydrogen bonds 14.9% of all protein-DNA interactions 70% are with the DNA backbone, mostly

    phosphate group Interactions with purine are common than with

    pyrimidine Polar and charged amino acids are frequently

    used: Arg, Lys, Asp, Glu, Ser and Thr

  • 3. Water mediated bonds Nearly as common as direct

    hydrogen bonds 14.9% of all protein-DNA

    interactions 70% are with the DNA

    backbone, mostly phosphate group

    Interactions with purine are common than with pyrimidine

    Polar and charged amino acids are frequently used: Arg, Lys, Asp, Glu, Ser and Thr

  • Summery Amino acids Mode of interaction Recognized base

    Hydrogen bond Arg, Lys His Ser

    Asn Gln Asp, Glu Van der waals contacts Phe, Pro Thr Gly, Ala, Val, Leu, Iso, Tyr

    No Base contact Cys, Met, Trp

    Multiple-donor Multiple-donor (bifurcate) Multiple-donor (bifurcate) Acceptor + donor Acceptor + donor Multiple-acceptor

    Ring-stacking Methyl contact

    G/complex G G Complex A/complex Complex

    A, T T Many (nonspecific)

  • Figure 2

    Trends in Biochemical Sciences 2014 39, 381-399DOI: (10.1016/j.tibs.2014.07.002) Copyright 2014 Elsevier Ltd Terms and Conditions

    Base and shape readout contribute to TFDNA binding specificity. (A) Base readout describes direct interactions between amino acids and the functional groups of the bases. Whereas the pattern of hydrogen bond acceptors (red) and donors (blue), heterocyclic hydrogen atoms (white) and the hydrophobic methyl group (yellow) is base pair-specific in the major groove, the pattern is degenerate in the minor groove. (B) Shape readout includes any form of structural readout based on global and local DNA shape features, including conformational flexibility and shape-dependent electrostatic potential. The DNA target of the IFN- enhanceosome (PDB ID 1t2k; top) varies in m i n o r g r o o v e s h a p e . T h e h u m a n papillomavirus E2 protein binds to a DNA binding site (PDB ID 1jj4; bottom) with intrinsic curvature. (C) Most DNA-binding proteins use interplay between the base- and shape-readout modes to recognize their DNA binding sites. However, the contribution of each mechanism to protein-DNA binding specificity might vary across TF families. Shape readout dominates for the minor groove-binding high motility group (HMG) box protein (PDB ID 2gzk; left). Base readout is a major contribution in DNA recognition by the bHLH protein Pho4 (PDB ID 1a0a; right). Both readout modes are more or less equally present in the DNA binding of a HoxExd heterodimer (PDB ID 2r5z; center).

  • Ejemplos de contactos DNA Protena

  • Los contactos pueden ser por dos una cara del DNA

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.24 Helix-turn-helix proteins use one helix to bind in the major groove while the other supports that binding through hydrophobic interacLon. Redrawn from Alberts, B., Bray, D., Lewis, J., Ra, M., Roberts, K., and Watson, J. Molecular Biology of the Cell. New York: Garland, 1994.

    Represor lac

    Factores con Homeodominios

  • Los dedos de Zn se estabilizan por el metal

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.25 Two dierent Zn nger moLfs are found in transcripLon factors. (a) Reproduced with permission from Voet, D., and Voet, J. G. Biochemistry, 2d ed. New York: Wiley, 1995. (1995) John Wiley & Sons, Inc. Part (b) and (c) generously supplied by C. Pabo, M.I.T.

    TFIIIA, SP1, Gal4, Superfamilia de receptores hormonales esteroideos

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.26 Leucine zipper proteins bind to DNA as dimers. Modied from Alberts, B., Bray, D., Lewis, J., Ra, M., Roberts, K., and Watson, J. Molecular Biology of the Cell. New York: Garland, 1994.

    Fos

    Jun

    CREB

  • Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin 2011 John Wiley & Sons, Inc.

    Figure 8.27 TranscripLon factor dimer formaLon is mediated through helix loop helix interacLons. Modied from Alberts, B., Bray, D., Lewis, J., Ra, M., Roberts, K., and Watson, J. Molecular Biology of the Cell. New York: Garland, 1994.

  • Ejemplo de unin no especfica: estructura del Nucleosoma

  • Figure 1

    Trends in Biochemical Sciences 2014 39, 381-399DOI: (10.1016/j.tibs.2014.07.002) Copyright 2014 Elsevier Ltd Terms and Conditions

    Structure-based illustration of multiple levels of TFDNA binding specificity. (A) The basic helix-loop-helix (bHLH) MadMax heterodimer (PDB ID 1nlw) binds to only a subset of putative DNA binding sites (blue). Some TFBSs are inaccessible owing to

    nucleosome formation (PDB ID 1kx5), whereas other accessible TFBSs are not selected by the TF. (B) Higher-order determinants of TF binding include cooperativity with cofactors (e.g., HoxExd heterodimer; PDB ID 2r5z), multimeric binding (e.g., p53

    tetramer; modeled based on PDB IDs 2ady and 1aie [228]), cooperativity through TFTF interactions (e.g., IFN- enhanceosome; modeled based on PDB IDs 1t2k, 2pi0, 2o6g and 2o61 [59]), and chromatin accessibility due to nucleosome formation (PDB ID

    1kx5) [229].

  • Reference

    N.M. Luscombe et al, Nucl. Acid Res 29, 2860-2874 (2001).

    Luger et al, Nature 389, 251-260 (1997)