Amino/Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?

Mitchell, John B. O.; Nandi, C. Lilian; McDonald, Ian K.; Thornton, Janet M.; Price, Sarah L.

doi:10.1006/jmbi.1994.1370

Cited by 310 publications

(177 citation statements)

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“…As we showed with reduced amino acid alphabets, the use of different definitions could lead to diverging results [123]. Distribution of the privileged interactions shows expected results, like the importance of Cysteine and of aromatic residues [105,106,[124][125][126][127][128][129][130]. Specificities are found according to the distance in the sequence between residues in contact.…”

Section: Discussionmentioning

confidence: 89%

Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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To cite this version:Guilhem Faure, Aurélie Bornot, Alexandre De Brevern. Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts. Biochimie, Elsevier, 2008, 90 (4) AbstractThree-dimensional structures of proteins are the support of their biological functions.Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-C distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria.First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted.Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues.Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SSCOMP) on the distribution of contacts.The prediction rates of these different methods are quite similar. However, using a distance criterion between side-chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed.Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviors distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease.

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Section: Discussionmentioning

confidence: 89%

Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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“…36 Van der Waals and hydrophobic contacts along the cation side chain contribute to the favorable energetics of the Arg-Trp pair, along with charge delocalization which maximizes Arg's interaction with Trp's indole ring. In addition, Arg often forms conventional hydrogen bonds with other residues while simultaneously interacting with Trp, [38][39][40] as seen in the activation-dependent interaction of R208 with E245 just next to Switch III, which allosterically links changes in nucleotide binding to Switch III conformation in Ga i proteins.…”

Section: Discussionmentioning

confidence: 99%

Trp fluorescence reveals an activation‐dependent cation‐π interaction in the Switch II region of Gα_i proteins

et al. 2009

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Crystal structures of Ga i (and closely related family member Ga t ) reveal much of what we currently know about G protein structure, including changes which occur in Switch regions. Ga t exhibits a low rate of basal (uncatalyzed) nucleotide exchange and an ordered Switch II region in the GDP-bound state, unlike Ga i , which exhibits higher basal exchange and a disordered Switch II region in Ga i GDP structures. Using purified Ga i and Ga t , we examined the intrinsic tryptophan fluorescence of these proteins, which reports conformational changes associated with activation and deactivation of Ga proteins. In addition to the expected enhancement in tryptophan fluorescence intensity, activation of GaGDP proteins was accompanied by a modest but notable red shift in tryptophan emission maxima. We identified a cation-p interaction between tryptophan and arginine residues in the Switch II of Ga i family proteins that mediates the observed red shift in emission maxima. Furthermore, amino-terminal myristoylation of Ga i resulted in a less polar environment for tryptophan residues in the GTPase domain, consistent with an interaction between the myristoylated amino terminus and the GTPase domain of Ga proteins. These results reveal unique insights into conformational changes which occur upon activation and deactivation of G proteins in solution.

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“…Another possibility is that certain geometries avoid disrupting hydrogen bonds to other groups. 22 There may also be other important effects: certain interaction geometries may allow more efficient packing or favor burial of hydrophobic residues. In a small number of cases, both residues will ligate a single metal ion, a situation that would naturally influence their interplanar angles.…”

Section: Possible Origins Of Non-randomnessmentioning

confidence: 99%

Non-randomness in side-chain packing: the distribution of interplanar angles

1997

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We analyze the distributions of interplanar angles between interacting side chains with well-defined planar regions, to see whether these distributions correspond to random packing or alternatively show orientational preferences. We use a non-homologous set of 79 high-resolution protein chain structures to show that the observed distributions are significantly different from the sinusoidal one expected for random packing. Overall, we see a relative excess of small angles and a paucity of large interplanar angles; the difference between the expected and observed distributions can be described as a shift of 5% of the interplanar angles from large (> or = 60 degrees) to small (< 30 degrees) values. By grouping the residue pairs into categories based on chemical similarity, we find that some categories have very non-sinusoidal interplanar angle distributions, whereas other categories have distributions that are close to sinusoidal. For a few categories, observed deviations from a sinusoidal distribution can be explained by the electrostatic anisotropy of the isolated pair potential energy. In other cases, the observed distributions reflect the longer range effects of different possible interaction geometries. In particular, geometries that disrupt external hydrogen bonding are disfavored.

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Amino/Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?

Cited by 310 publications

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Protein contacts, inter-residue interactions and side-chain modelling

Protein contacts, inter-residue interactions and side-chain modelling

Trp fluorescence reveals an activation‐dependent cation‐π interaction in the Switch II region of Gα_i proteins

Non-randomness in side-chain packing: the distribution of interplanar angles

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Amino/Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?

Cited by 310 publications

References 0 publications

Protein contacts, inter-residue interactions and side-chain modelling

Protein contacts, inter-residue interactions and side-chain modelling

Trp fluorescence reveals an activation‐dependent cation‐π interaction in the Switch II region of Gαi proteins

Non-randomness in side-chain packing: the distribution of interplanar angles

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Trp fluorescence reveals an activation‐dependent cation‐π interaction in the Switch II region of Gα_i proteins