C-h⋯π-interactions in proteins

Brandl, Maria T.; Weiss, M.S.; Jabs, Andreas; Sühnel, Jürgen; Hilgenfeld, Rolf

doi:10.1006/jmbi.2000.4473

Cited by 583 publications

(539 citation statements)

References 56 publications

Supporting

Mentioning

491

Contrasting

Unclassified

Order By: Relevance

“…Indeed, these authors studied the number of occurrence of contacts whereas we analyzed the preferences by the use of the relative frequencies. Thus, they did not see the significance of aromatic interactions for near contacts as it was shown in other studies [23]. In the same way, prediction of side-chain positioning also shows strong divergences;…”

Section: Discussionmentioning

confidence: 65%

“…Hydrogen bonds are formed by the "sharing" of a hydrogen atom between two electronegative atoms such as N and O, participate in the formation of regular secondary structures [21]. It has also been shown in many studies that even weak hydrogen bonds could be essential for inter-residue contacts [22][23][24]. Ionic bonds involve interactions between oppositely charged groups of a molecule, e.g.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 65%

Section: Introductionmentioning

confidence: 99%

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

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

View full text Add to dashboard Cite

show abstract

“…The P1 cyclohexyl ring is in a chair conformation and makes van der Waals interactions with tyrosine residues 150 and 161. The latter interaction possibly involves a C-H··· π hydrogen bond 85,86 of ~3.3…”

Section: P1 Residuementioning

confidence: 99%

Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus NS2B–NS3 Protease

et al. 2013

Self Cite

View full text Add to dashboard Cite

A series of new substrate analogue inhibitors of the WNV NS2B–NS3 protease containing decarboxylated arginine mimetics at the P1 position was developed. Among the various analogues, trans‐(4‐guanidino)cyclohexylmethylamide (GCMA) was identified as the most suitable P1 residue. In combination with dichloro‐substituted phenylacetyl groups at the P4 position, three inhibitors with inhibition constants of <0.2 μM were obtained. These GCMA inhibitors have a better selectivity profile than the previously described agmatine analogues, and possess negligible affinity for the trypsin‐like serine proteases thrombin, factor Xa, and matriptase. A crystal structure in complex with the WNV protease was determined for one of the most potent inhibitors, 3,4‐dichlorophenylacetyl‐Lys‐Lys‐GCMA (Ki=0.13 μM). The inhibitor adopts a horseshoe‐like conformation, most likely due to a hydrophobic contact between the P4 phenyl ring and the P1 cyclohexyl group, which is further stabilized by an intramolecular hydrogen bond between the P1 guanidino group and the P4 carbonyl oxygen atom. These inhibitors are stable, readily accessible, and have a noncovalent binding mode. Therefore, they may serve as suitable lead structures for further development.

show abstract

“…52,53 In P2.2 and P2.3, we used 'WY' and 'FY' to substitute 'FF' in the first and second 'FFRR' units, respectively, to make the N-terminus less hydrophobic (but still hydrophobic overall). Additionally, stabilizing the last helix was facilitated by 2 'AH' substitutions of 'FF', as Ala is able to significantly stabilize helices in short peptides [54][55][56] and His has been found to increase the stability of helices by Hbonding.…”

Section: Balanced Hydrophobic and Hydrophilic Residue Repeating Sequementioning

confidence: 99%

Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10

Wang

Cummins

et al. 2016

Human Vaccines & Immunotherapeutics

View full text Add to dashboard Cite

Interleukin 10 (IL-10) is a cytokine that is able to downregulate inflammation. Its overexpression is directly associated with the difficulty in the clearance of chronic viral infections, such as chronic hepatitis B, hepatitis C and HIV infection, and infection-related cancer. IL-10 signaling blockade has been proposed as a promising way of clearing chronic viral infection and preventing tumor growth in animal models. Recently, we have reported that peptides with a helical repeating pattern of hydrophobic and hydrophilic residues are able to inhibit IL-10 significantly both in vitro and in vivo. 1 In this work, we seek to further study the inhibiting mechanism of these peptides using sequence-modified peptides. As evidenced by both experimental and molecular dynamics simulation in concert the N-terminal hydrophobic peptide constructed with repeating hydrophobic and hydrophilic pattern of residues is more likely to inhibit IL10. In addition, the sequence length and the ability of protonation are also important for inhibition activity.

show abstract

C-h⋯π-interactions in proteins

Cited by 583 publications

References 56 publications

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

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

Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus NS2B–NS3 Protease

Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10

Contact Info

Product

Resources

About