Category: BIOCHEMISTRY

[NEW] T. Kobayashi, R. Yanagita, K. Irie, Bioorg. Med. Chem. Lett. 2020, 30, 127657: Synthesis and biological activities of simplified aplysiatoxin analogs focused on the CH/π interaction.

[NEW] M. Ozawa et al., J. Mol. Graph. Model. 2017, 75, 117–124: The role of CH/pi interactions in the high affinity binding of streptavidin and biotin.

C. Di Scala et al., Biochemistry, 2014, 53, 4489–4502: Interaction of Alzheimer’s β-Amyloid Peptides with Cholesterol: Mechanistic Insights into Amyloid Pore Formation.

A. K. Pandey et al., Biochemistry, 2014, 53, 5307–5314: Tunable Control of Polyproline Helix (PPII) Structure via Aromatic Electronic Effects: An Electronic Switch of Polyproline Helix.

Y.- K. Kang, I.-K. Yoo, Biopolymers 2014 in press; DOI: 10.1002/bip.22507: Influence of Substituents on Conformational Preferences of Helix Foldamers of c-Dipeptides.

M. Kumar, P. J. Balaji, J. Mol. Model. 2014, 20, 2136: C-H/π interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability.

C. Di Scala et al., Biochemistry 2014, DOI: 10.1021/bi500373k: Interaction of Alzheimer’fs β-Amyloid Peptides with Cholesterol: Mechanistic Insights into Amyloid Pore Formation.

[NEW] H. D. Hickman and J. W. Yewdell, Eur. J. Immunol. 2013, 43, 2814-2817: Going Pro to enhance T-cell immunogenicity: Easy as π?

R. U. Kadam et al., ACS Chem. Biol. 2013, 8, 1925–1930: CH−|π “T-Shape” Interaction with Histidine Explains Binding of Aromatic Galactosides to Pseudomonas aeruginosa Lectin LecA.

T. Ema et al., Org. Biomol. Chem. 2012, 10, 6299-6308: Redesign of enzyme for improving catalytic activity and enantioselectivity toward poor substrates: manipulation of the transition state.

M. V. Cherrier et al., Journal of Biological Inorganic Chemistry, 2012, 17, 817-829: The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.

Y. K. Kang, B. J. Byun, Biopolymers. 2012, 97, 778-788. doi: 10.1002/bip.22062: Strength of CH/pi interactions in the C-terminal subdomain of villin headpiece.

T. Ema et al., Chem. Commun. 2010, 46, 5440–5442: Rational creation of mutant enzyme showing remarkable enhancement of catalytic activity and enantioselectivity toward poor substrates.

R. K. Raju et al., Phys. Chem. Chem. Phys. 2010, 12, 7117-7125: Modelling the binding of HIV-reverse transcriptase and nevirapine: an assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding.

D. Solis et al., Int. J. Biochem. Cell Biol. 2010, 42, 1019-1029: N-domainofhumanadhesion/growth-regulatorygalectin-9:Preferencefor distinctconformersandnon-sialylatedN-glycansanddetectionof ligand-inducedstructuralchangesincrystalandsolution .

I.-H. Park, C. Li, J. Molec. Recogn. 2010, 23, 1-12: Characterization of molecular recognition of STAT3 SH2 domain inhibitors through molecular simulation.

N. Yahi et al., PLoS One. 2010; 5(2): e9079: doi: 10.1371: How Cholesterol Constrains Glycolipid Conformation for Optimal Recognition of Alzheimer's ? Amyloid Peptide (Abeta1-40).

K. Kar et al., Biochemistry 2009, 48, 7959-7968: Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures.

Y. Ferrand et al., Angew. Chem. Int. Ed. 2009, 48, 1775-1779: A synthetic lectin for O-linked beta-N-acetylglucosamine.

A. F. Neuwald, BMC Structural Biology 2009, 9: 11: doi:10.1186/1472-6807-9-11: The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.

J. Fantini et al., Biochim. Biophys. Acta - Biomembranes 2009, 1788, 2345-2361: Sphingolipid/cholesterol regulation of neurotransmitter receptor conformation and function.

[NEW] M. Maresca et al., Phys. Chem. Chem. Phys. 2008, 10, 2792–2800: Controlled aggregation of adenine by sugars: physicochemical studies, molecular modelling simulations of sugar-aromatic CH/pi stacking interactions, and biological significance.

M. Maresca et al., Phys. Chem. Chem. Phys. 2008, 10, 2792-2800: Controlled aggregation of adenine by sugars: physicochemical studies, molecullar modelling simulations of sugar-aromatic CH-pi stacking interactions, and biological significance.

R. C. Yanagita et al., J. Med. Chem. 2008, 51, 46-56: Synthesis, conformational analysis, and biological evaluation of 1-hexylindolactam-V10 as a selective activator for novel protein kinase C isozymes.

K. P. Kursula et al., J. Mol. Biol. 2008, 375, 270-290: High-resolution structural analysis of mammalian profilin 2a complex formation with two physiological ligands: the formin homology 1 domain of mDia1 and the proline-rich domain of VASP.

H. Mukaiyama et al., Bioorg. Med. Chem. 2008, 16, 909-921: Novel pyrazolo[1,5-a]pyrimidines as c-Src kinase inhibitors that reduce IKr channel blockade.

M. Cohen et al., Proteins 2008, 72, 741-753: Similar chemistry, but different bond preferences in inter versus intra-protein interactions.

P. Chakrabarti, R. Bhattacharyya, Prog. Biophys. Mol. Biol. 2007, 95, 83-137: Geometry of nonbonded interactions involving planar groups in proteins. [Review]

G. Toth et al., Current Pharmac. Design 2007, 13, 3476-3430: The Role and Significance of Unconventional Hydrogen Bonds in Small Molecule Recognition by Biological Receptors of Pharmaceutical Relevance. [Review]

R. C. Yanagita et al., Heterocycles 2007, 73, 289-302: Binding selectivity of 1- or 12-substituted indolactam derivatives for protein kinase C isozymes.

G. Toth et al., Biochemistry 2006, 45, 6606-6614: Flap closing of HIV-1 protease due to the binding of substrate: a model for flap closing mechanism in retroviral aspartic proteases.

G. Toth, A. Borics, J. Mol. Modeling, Graphics 2006, 24, 465-474: The mechanism of flap opening of HIV-1 Protease.

J. Flint et al., J. Biol. Chem. 2005, 280, 23718-23726: Probing the mechanism of ligand recognition in family 29 carbohydrate-binding modules.

F. C. Acher, H.-O. Bertrand, Biopolymers 2005, 80, 357-366: Amino acid recognition by venus flytrap domains is encoded in an 8-residue motif.

V. Spiwok et al., Carbohydr. Res. 2004, 339, 2275-2280: Role of CH/pi interactions in substrate binding by Escherichia coli beta-galactosidase.

A. Bernardi et al., Chem. Eur. J. 2004, 4395-4406: Intramolecular carbohydrate-aromatic interactions and intermolecular van der Waals interactions enhance the molecular recognition ability of GM1 glycomimetics for cholera toxin.

K. Watanabe et al., Bull. Chem. Soc. Jpn. 2004, 77, 543-548: How does lipase flexibility affect its enantioselectivity in organic solvents? A possible role of CH...pi association in stabilization of enzyme-substrate complex.

T. Kinoshita et al., FEBS Lett. 2004, 556, 43-46: Inhibitor-induced structural change of the active site of human poly(ADP-ribose) polymerase.

D. J. Reinert et al., Chem. & Biol. 2004, 121-126: Conversion of squalene to the pentacarbocyclic hopene.

V. Kulsak et al., Chem.& Biol. 2003, 10, 331-340: Sexual Attraction in the Silkworm Moth: Nature of Binding of Bombykol in Pheromone Binding Protein - An Ab Initio Study.

P. Carnevali et al., J. Am. Chem. Soc. 2003, 125, 14244-14245:Protein Structure Predictions using Monte Carlo Simulations with Modal Moves.

A.-S. Bessis et al., Proc.NAS 2002, 99, 11097-11102: Closure of the venus flytrap module of mGlu8 receptor and the activation process: Insights from mutations converting antagonists into agonists.

M. T. Reetz, Current Opinion in Chemical Biology 2002, 6, 145-150: Lipases as practical biocatalysts.

L. Chen et al., Bioorg. Med. Chem. Lett. 2002, 12, 1679-1682: Focused library approach for identification of new N-acylphenylalanines as VCAM/VLA-4 antagonist.

A. Matsushima et al., Bull. Chem. Soc. Jpn. 2000, 73, 2531-2538: Exploration of the role of phenylalanine in the thrombin receptor tethered-ligand peptide by substitution with a series of trifliorophenylalanines.

K. Ohgi et al., Biosci., Biotechnol., Biochem.. 2000, 64, 2068-2074: Enzymatic properties of phenylalanine 101 mutant enzyme of ribonuclease Rh from Rhizopus niveus.

H. Fretz et al., Curr. Pharm. Design 2000, 6, 1777-1796: Structure-based design of compounds inhibiting Grb2-SH2 mediated protein-protein interactions in signal transduction pathways.

T. Watanabe et al., Tetrahedron 2000, 56, 741-752: Structure-activity relationship and rational design of 3,4-dephostatin derivatives as protein tyrosine phosphate inhibitors.

A. Matsushima et al., J. Biochem. 2000, 128, 225-232: Edge-to-face CH/pi interaction between ligand Phe-phenyl and receptor aromatic group in the thrombin receptor activation.T. Fujita et al., Tetrahedron Lett. 2000, 41, 923-927: Synthesis of a complete set of L-difluorophenylalanines, L-(F-2)Phe, as molecular explorers for the CH/pi interaction between peptide ligand and receptor.

C. Kubli-Garfias et al., THEOCHEM 2000, 529, 203-208: Electronic structure of gonadotropin-releasing hormone (GnRH): a semiempirical study.

S. Ueji et al., Biochem. Lett. 1999, 21, 865-868: Lipase-catalyses esterification of 2-(4-substituted phenoxy)propionic acids in organic solvents: substituent effect controlling enantioselectivity toward racemic acids.

M. L. Barreca et al., Bioorg. Med. Chem. Lett. 1999, 7, 2283-2292: Comparative molecular field analysis (CoMFA) and docking studies of non-nucleoside HIV-1 RT inhibitors (NNIs).

Y. Shimohigashi et al., Biopolymers 1999, 51, 9-17: Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pi interaction.

J. Schoepfer et al., Bioorg. Med. Chem. Lett. 1999, 7, 221-226: Highly potent inhibitors of the Grb2-SH2 domain.

T. Nose et al., J. Biochem. 1998, 124, 354-358: Interaction mode of the Phe-phenyl group of thrombin receptor-tethered ligand SFLLRNP in receptor activation.

T. Sato et al., Biosci. Biotech. Biochem. 1998, 62, 407-411: Overexpression of squalene-hopene cyclase by the pet vector in E. coli and first identification of Trp and Asp residues inside the QW motif as active-sites.

Y. Inoue et al., J. Hypertension 1997, 15, 703-714 : A review of mutagenesis studies of angiotensin II type 1 receptor, the three-dimensional receptor model in search of the agonist and antagonist binding site and the hypothesis of a receptor activation mechanism [REVIEW].

T. Kawasaki et al., Chem. Lett. 1997, 351-352: The mode of substrate-recognition mechanism of arylmalonate decarboxylase.

T. Kawasaki et al., Bull. Chem. Soc. Jpn. 1996, 69, 3591-3594: On the conformation of the substrate binding to the active site during the course of enzymatic decarboxylation

S. Kanzler et al., Bioorg. Med. Chem. Lett. 1996, 6, 1865-1868: A novel class of vitamin D analogs. Synthesis and preliminary biological evaluation.

I. Maeda et al., J. Biochem. 1996, 119, 870-877: Chymotripsin inhibition induced by side chain-side chain intramolecular CH/pi interaction.

I. Maeda et al., Biochem. Biophys. Res. Commun. 1993, 193, 428-433: Water-soluble chymotripsin specific inhibitors containing arginine.

N. Morisaki et al., Eur. J. Biochem. 1993, 211, 111-115: Effect of side-chain structure on inhibition of yeast fatty-acid synthase by cerulenin analogues.

D. H. Kim et al., Bioorg. Med. Chem. 1998, 6, 239-249; A novel type of structurally simple nonpeptide inhibitors for α-chymotrypsin. Induced-fit binding of methyl 2-allyl-3-benzene-propanoate to the S2 subsite pocket

Y. Shimohigashi et al., J. Chem. Soc., Perkin Trans. 1 1996, 2479-2485: Chymotrypsin inhibitory conformation induced by amino acid side chain–side chain intramolecular CH/π interaction.