Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization

Burley, S.K.; Petsko, Gregory A.

doi:10.1126/science.3892686

Cited by 2,439 publications

(1,739 citation statements)

References 25 publications

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“…We found that the main reason for this behavior was the carbon-carbon function u ab (r ab ) of eqn (3). Therefore, for r ab r r max , where r max is the point where u CC reaches its maximum, this function was set to a constant value, equal to its value at r max E 2.5 Å .…”

Section: A Analytic Fitmentioning

confidence: 99%

“…The interactions between aromatic systems are of special interest, since they can play an important role in determining protein and DNA stability [1][2][3][4] and DNA-protein interaction. 5,6 The benzene dimer has received much attention both from experimentalists [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] and theorists.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Avoird

Podeszwa

Szalewicz

et al. 2010

Phys. Chem. Chem. Phys.

152

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An improved intermolecular potential surface for the benzene dimer is constructed from interaction energies computed by symmetry-adapted perturbation theory, SAPT(DFT), with the inclusion of third-order contributions. Twelve characteristic points on the surface have been investigated also using the coupled-cluster method with single, double, and perturbative triple excitations, CCSD(T), and triple-zeta quality basis sets with midbond functions. The SAPT and CCSD(T) results are in close agreement and provide the best representation of these points to date. The potential was used in calculations of vibration-rotation-tunneling (VRT) levels of the dimer by a method appropriate for large amplitude intermolecular motions and tunneling between multiple equivalent minima in the potential. The resulting VRT levels were analyzed with the use of the permutation-inversion full cluster tunneling (FCT) group G 576 and a chain of subgroups that starts from the molecular symmetry group C s (M) of the rigid dimer at its equilibrium C s geometry and leads to G 576 if all possible intermolecular tunneling mechanisms are feasible. Further information was extracted from the calculated wave functions. It was found, in agreement with the experimental data, that for all of the 54 G 576 symmetry species (with different nuclear spin statistical weights) the lower VRT states have a tilted T-shape (TT) structure; states with the parallel-displaced structure are higher in energy than the ground state of A + 1 symmetry by at least 30 cm À1 . The dissociation energy D 0 equals 870 cm À1 , while the depth D e of the TT minimum in the potential is 975 cm À1 . Hindered rotation of the cap in the TT structure and tilt tunneling lead to level splittings on the order of 1 cm À1 . Also intermolecular vibrations with excitation energies starting at a few cm À1 were identified. A further small, but probably significant, level splitting was assigned to cap turnover, although in scans of the potential surface we could not find a plausible 'reaction path' for this process. Rotational constants were extracted from energy levels calculated for total angular momentum J = 0 and 1, and from expectation values of the inertia tensor. Although the end-over-end rotational constant B + C agrees well with the measured microwave spectra, there is disagreement with the measurements concerning the (a)symmetric rotor character of the benzene dimer. It is concluded from calculations for the 54 nuclear spin species that the microwave spectrum should show overlapping contributions from many different species. Another interesting conclusion regards the role of the quantum number K, for a prolate near-symmetric rotor the projection of the total angular momentum on the prolate axis. For the benzene dimer, K has a substantial effect on the energy levels associated with the intermolecular motions of the complex.

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Section: A Analytic Fitmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Avoird

Podeszwa

Szalewicz

et al. 2010

Phys. Chem. Chem. Phys.

152

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“…Furthermore, peptides that contain Asx turns require Pro to further support the unique turn conformation. The surprising stability of F4-Asn suggests other stabilizing factors such as Tyr aromaticaromatic interactions (Burley & Petsko, 1985) or Tyr phenolic hydrogen bonding to a charged side chain may be involved in stabilizing this peptide as suggested for F4-6.…”

Section: Discussionmentioning

confidence: 91%

“…Because precedent shows that a Tyr interaction is possible with Glu in a helix (Ramachandran et al, 1971), Asp may impose the same restrictions here as it does when hydrogen bonding with Lys, i.e., interacting more favorably in an aL-helical conformation. Lastly, the high content of Tyr residues may further enhance the stability of the lefthanded helix by aromatic-aromatic interactions (Burley & Petsko, 1985).…”

Section: Discussionmentioning

confidence: 99%

Structure of synthetic peptide analogues of an eggshell protein of Schistosoma mansoni

et al. 1993

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The peptide (Gly-L-Tyr-L-Asp-L-Lys-L-Tyr),, referred to as F4-6, was synthesized as a model for a schistosome eggshell protein in which the Gly-Tyr-Asp-Lys-Tyr consensus sequence is repeated over 40 times. Analysis by CD, Fourier transform infrared spectroscopy, potentiometric and spectrophotometric titrations, NMR, and molecular modeling suggests that F4-6 forms some type of left-handed structure. A likely possibility appears to be a lefthanded a-helix stabilized by Lysj-Aspj+, salt bridges and possibly Aspj-Tyrj+, hydrogen bonding and Tyr-Tyr interactions. Spectroscopic studies of a number of F4-6 analogues support this conclusion. For example, substitution of D-Ala for Gly produces a peptide with enhanced left-handed helical spectral characteristics, whereas an L-Ala substitution results in a peptide with minimal structure. These studies suggest that the F4 protein from Schistosoma mansoni may be the first example of a naturally occurring protein devoid of proline and carbohydrate that forms a left-handed helix composed of L-amino acids, although alternative forms of other left-handed structures have yet to be rigorously excluded.Keywords: F4-6 peptide; Schistosoma mansoni; schistosome eggshell protein The pathology of schistosomiasis is due to the inflammatory response to the eggs of the parasitic trematode, Schistosoma mansoni (or other closely related schistosomes) lodged in the hosts' body tissues. Granulomas form around the eggs in response to soluble carbohydrate and protein antigens secreted by the eggs. When an egg is deposited by the female schistosome, it contains a fertilized ovum and 30-40 vitelline cells. Development of the miracidium larva occurs inside the eggshell lodged in the host tissues. The eggshell is formed shortly before egg laying from protein precursors secreted by the vitelline cells that subsequently become surrounded by the eggshell. These vitelline cells serve as a food supply for the developing miracidium and disappear before hatching. The secreted

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“…An increasing body of evidence indicates that the ability of aromatic rings to serve as hydrogen-bond acceptors is real and significant to the structure and function of proteins (Burley & Petsko, 1985;Levitt & Perutz, 1988). Our work suggests that highly inaccurate simulations may result if the capacity to form such bonds is not incorporated into aromatic models.…”

Section: (Ps)mentioning

confidence: 90%

Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements

Axelsen¹,

Gratton²,

Prendergast³

1991

Biochemistry

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ABSTRACT:The fluorescence anisotropy decay of the single tryptophan residue in phospholipase A2 was studicd by use of differential polarized phase fluorometry and computer simulations of protein dynamics. The results enable the verification of a simulated dynamic event by direct experimental measurement on thc same time scale. When all hydrogen atoms are modeled explicitly, the simulations agree well with the experimental measurements. However, the measurements contradict simulations in which nonpolar hydrogens are incorporated into "extended" or "united" atoms. These simulations predict an anisotropy decay in excess of mcasured values and appear to seriously underestimate the electrostatic interactions occurring between water and aromatic side chains. The results support the general validity of studying protein dynamics with

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Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization

Cited by 2,439 publications

References 25 publications

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Vibration–rotation-tunneling states of the benzene dimer: an ab initio study

Structure of synthetic peptide analogues of an eggshell protein of Schistosoma mansoni

Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements

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