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College 3. Macromoleculen en biomoleculen. Maar eerst: elektron configuratie Cytosine. The answer: only with A & T and with C & G are there opportunities to establish hydrogen bonds (shown here as dotted lines) between them (two between A & T; three between C & G).
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College 3 Macromoleculen en biomoleculen
The answer: only with A & T and with C & G are there opportunities to establish hydrogen bonds (shown here as dotted lines) between them (two between A & T; three between C & G). These relationships are often called the rules of Watson-Crick base pairing, named after the two scientists who discovered their structural basis. The rules of base pairing tell us that if we can "read" the sequence of nucleotides on one strand of DNA, we can immediately deduce the complementary sequence on the other strand. DNA base pairing • A with T: adenine (A) always pairs with thymine (T) • C with G: cytosine (C) always pairs guanine (G) • This is consistent with there not being enough space (20 Å) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. • But why not A with C and G with T?
The hydrogen bond Fig. 2.2.5.A hydrogen bond between two water molecules. The strength of the interaction is maximal when the O-H covalent bond points directly along a lone-pair electron cloud of the oxygen atom to which its hydrogen bonded. In het algemeen: D—H · · · ·A The large electronegativity difference between H and O confers a 33% ionic character on the OH-bond as reflected by water’s dipole of 1.85 debye units. → highly polar molecule The electrostatic interactions between the dipoles of two water molecules tend to orient them such that the O-H bond on one molecule points towards a lone pair electron cloud on the oxygen atom of the other water molecule
The hydrophobic interaction Because these cage structures are more ordered than the surrounding water, their formation increases the free energy. This free energy cost is minimized, however, if the hydrophobic (or hydrophobic parts of amphipathic molecules) cluster together so that the smallest number of water molecules is affected.
Macromolecules and BiomoleculesLevels of structure Natural and synthetic polymers Primary structure: sequence of small molecular residues that make up the polymer proteins are formed from 20 different amino acids strung together by the peptide bond, -CONH- (see below). The determination of the primary structure is called ‘sequencing’. The secondary structure of a macromolecule is the (often local) spatial arrangement of a chain random coil, helices, sheets The tertiary structure is the overall three-dimensional structure of a macromolecule The quarternary structure of a macromolecule is the manner in which large molecules are formed by aggregation
Random coil • The most likely conformation of a chain of identical subunits not capable of forming H-bonds or any other type of specific bond is a random coil. Polyethylene is a simple example. The random coil model is a helpful starting point for estimating the orders of magnitude of the hydrodynamic properties of polymers and denatured proteins in solution. The simplest model of a random coil is a freely jointed chain, in which any bond is free to make any angle with respect to the preceding one (fig 3.3)
The Structure of Proteins Proteins are the ‘hydrogen atoms’ of life. (Un-)Fortunately there are many of them, all of them have a specific function and as a consequence we have to figure out the rules by generalizing their physical (and chemical and biological) properties. A protein is a polypeptide composed of covalently linked -amino acids, NH2CHRCOOH, where R is one of only twenty possible groups. The resulting sequence of R groups linked by peptide bonds for a large part determines the structure and function of the protein.
C = koolstof N = stikstof O = zuurstof H = proton R = een aminozuur Peptide α-helix Eiwit
The Structure of Proteins R = 20 different amino acids, ‘simple’ organic molecules composed of C, H, N, O and an occasional S. Nevertheless, the chemical properties of the various amino acid side chains vary from hydrophobic to polar to charged, from large to small, from flexible to rigid and these properties are used to add ‘functionality’ and ‘activity’ to a sequence of amino acids folded into a protein structure
The amino acids Fig 4. The basic, acidic, uncharged and non-polar sidechains. The uncharged polar side chains are often involved in hydrogen bonding. The hydrophobic side chains occur in the interior of a protein and their size and shape play an important role in the compactness of a protein. In regions where a-helices fold over one another small residues are required. Proline is special because it can not fit in the a-helix. Aromatic residues often have additional functions. For instance in photosystem 2 of photosynthesis a tyrosine plays a crucial role in electron and proton transfer. The S atoms in methionine and cysteine play important roles in cofactor binding and protein folding.
The electronic structure of the peptide bond Sequence → conformation → function Prediction of the conformation from the primary structure, the so-called protein folding problem, is extraordinarily difficult and is the focus of much research One major factor determining the secondary structure of proteins is found in the stabilization of certain structures by hydrogen bonds involving the peptide bond. For peptide structures Pauling and Corey (1951) proposed (without having ‘seen’ them, based on valence, LCAO, Huckel) that:
The four atoms involved, O, C, N, H lie in a relatively rigid plane. • The planarity is due to the delocalization of π-electrons over the N, C and O atoms and the maintenance of maximum overlap of the contributing π-orbitals. • Two types of structures exist, helices and sheets, where all NH and CO groups are engaged in hydrogen bonding. • The N, H and O atoms involved in H-bonds between different parts of a polypeptide chain lie in a (more or less) straight line (with displacements of H tolerated up to not more than 30o from the N-O vector. Fig. 4.9 The peptide bond, which is an essential part of the amino acid chain constituting a protein, is composed of the atoms O, C, N, H, which all are positioned in one plane. Also the two a-carbon atoms flanking the peptide bond are in that plane. Consequently the configuration of the polypeptide backbone is described by two angles per residue indicated in the figure.
Peptide bonds Fig 4.10 Bond angles in the peptide bond. Note that all the angles are close to 120o, typical for sp2-hybridization. 1 π e 1 π e 2 π e O-atom: C-atom: N-atom:
Π orbitals.. linear combination of the orbitals, results in 3 π orbitals Accommodating the 4 π electrons Bonding energy from π electrons makes the peptide bond rigid and planar. Π network does not extend over Cα
The total energy of a protein and its energy landscape The simplest calculations of the conformational energy of a polypeptide. 1. Bond stretching. model a bond as a spring, then the potential energy takes the form of Hooke’s law and is given by: (4.16) 2. Bond bending. An O-C-H bond angle may open out or close in slightly to enable the molecule as a whole to better fit together. If the equilibrium bond angle is we write: (4.17) where is the bending force constant, a measure for how difficult it is to change the bond angle. Again this contribution must be summed over all bonds. 3. Bond torsion. (4.18) Because for a regular structure, like an -helix only two angles are needed to specify the conformation of that helix, and they range from -180o to +180o, the torsional potential energy of the entire molecule can be represented on a Ramachandran plot, a contour diagram in which one axis represents and the other represents .
For a right-handed α-helix and . Plus 4. Interaction between partial charges. 5. Dispersive and repulsive interactions, Lennard-Jones potential. 6. Hydrogen bonding.
α-helix Fig.4.13. The a-helix. A. Polypeptide backbone showing the arrangements of the H-bonds. The N-H of the peptide bond make an H-bond with the C=O of a peptide bond 3+ a bit residues further along the chain. And this pattern repeats for every next peptide bond in the chain. B. Ribbon diagram with the polypeptide backbone drawn in. C. The ribbon symbolizing the a-helix.
β-sheet Fig.4.20 The anti-parallel b-sheet. (D) The protein backbone showing the H-bonds between adjacent strains. (E) Ribbon diagram including the polypeptide backbone (F) Symbolic representation of the b-sheet.
Antiparallel and parallel β-sheet The energetically preferred dihdreal angles are (φ, ψ) = (–135°, 135°) (φ, ψ) about (–140°, 135°) (φ, ψ) about (–120°, 115°)
Anti-parallel β-sheet The second most-frequently occurring element of secondary structure is the antiparallel β-sheet. The N-H and C=O groups of a certain strand are hydrogen bonded to C=O and N-H groups of adjacent chains that run parallel to it, but in the opposite direction. The R-side groups in each strand alternately project above and below the plane of the sheet (see fig 4.20)
Anti-parallel β-sheet example: fibroin Fig 4.21 Silk fibroin is organized in an anti-parallel b-sheet.
Een voorbeeld: Photoactive Yellow Proteinblue-light sensor from H. halophila Tyr42 Glu46 chromophore Cys69 Thr50 Absorption of a blue-light photon triggers the photocycle
Experimental methods • Site directed mutagenesis • P68 P68V, P68A, P68G • Ultrafast spectroscopy of • WT and mutants (VIS and mid-IR) • Molecular dynamics simulations • WT and mutants (ground state)
Simultaneous target analysis of all samples -Identical spectra -Different dynamics *wt fastest, p68v, p68a, p68g -Different quantum yield *wt most effective, p68v, p68a,p68g
Distributions of H-bonds with different strengths Mid-IR: t=0 spectra
