Category: PROTEIN

[NEW] K. Fukuzawa, T. Takagi, C. Watanabe et al, J. Phys. Chem. Lett. 2021, 12, 4059−4066: Intermolecular Interaction Analyses on SARS-CoV‐2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation.

[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] G. Platzer, M. Mayer, Angew. Chem. Int. Ed. 2020, 132, 14971-14978:  PI by NMR: Probing CH–π Interactions in Protein–Ligand Complexes by NMR Spectroscopy.

J. Houser, J. Koca et al., Chem. Eur. J. 2020 https://doi.org/10.1002/chem.202000593: The CH‐π interaction in protein – carbohydrate binding: Bioinformatics and in vitro quantification.

J. Wu, Y. Deng, et al., Toxins 2019, 158: Multiple CH/π Interactions Maintain the Binding of Aflatoxin B₁ in the Active Cavity of Human Cytochrome P450 1A2.

M. Ozawa et al., J. Mol. Graph. Model 2017, 75, 73-82: Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

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.

K. K. Bisht et al., RSC Adv. 2014, 4, 7352–7360: Structural and functional studies on ternary coordination polymers from 5-bromoisophthalate and imidazole based flexible linker.

A. Miyanaga et al., J. Biol. Chem. 2014, doi: 10.1074/jbc.M114.602326: The crystal structure of the adenylation enzyme VinN reveals a unique β-amino acid recognition mechanism.

N. L. Zondlo, Acc. Chem. Res. 2012. DOI: 10.1021/ar300087y: Aromatic Proline Interactions: Electronically Tunable CH/pi Interactions.

Y. K. Kang, B. J. Byun, Biopolymers 2012, 97, 778-88. doi: 10.1002/bip.22062: Strength of CH/pi interactions in the C-terminal subdomain of villin headpiece.

W. Patrick et al., FEBS J. 2010, 277, 4549-4561: Carbohydrate binding sites in Candida albicans exo-b-1,3-glucanase and the role of the Phe-Phe clamp at the active site entrance.

M. J. Plevin et al., Nature Chemsitry 2010, 2, 466-471: Direct detection of CH/pi nteractions in proteins.

J. P. Yesudas et al., J. Mol. Model. 2010, DOI 10.1007/s00894-010-0736-2: Analysis of structural water and CH/pi interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT.

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).

M. Mauro et al., J. Med. Chem. 2010, 53, 230-240: X-ray Crystallographic Analysis of alpha-Ketoheterocycle Inhibitors Bound to a Humanized Variant of Fatty Acid Amide Hydrolase.

V. Voynov et al., PLoS One. 2009; 4: e8425. doi: 10.1371/journal.pone.0008425: Dynamic Fluctuations of Protein-Carbohydrate Interactions Promote Protein Aggregation.

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

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.

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

E. Polverini et al., Biochemistry 2008, 47, 267-282: Binding of the proline-rich segment of myelin basic protein to SH3 domains: spectroscopic, microarray, and modeling studies of ligand conformation and effects of posttranslational modifications.

R. K. Raju et al., Phys. Chem. Chem. Phys. 2008, 10, 6500-6508: Carbohydrate/protein recognition probed by density functional theory and ab initio calculations including dispersive interactions.

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.

B. Dasgupta et al., FEBS Lett. 2007, 581, 4529-4532: Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif.

A. Gil et al., J. Phys. Chem. B 2007, 111, 9372-9379: CH/pi interactions in DNA and proteins. A theoretical study.

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, 3476-3493: The Role and Significance of Unconventional Hydrogen Bonds in Small Molecule Recognition by Biological Receptors of Pharmaceutical Relevance. [Review]

M. S. Sujatha et al., J. Molec. Struct: THEOCHEM 2007, 814, 11-24: MP2/6-311++G(d,p) study on galactose-aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residue.

Y. Yamaguchi et al., J. Med. Chem. 2007, 50, 6647-6653: Crystallographic investigation of the inhibition mode of a VIM-2 metallo-beta-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor.

A. Okumura et al., FEBS Lett. 2007, 581, 5255-5258: Aromatic structure of Tyrosine-92 in the extrinsic PsbU protein of red algal Photosystem II is important for its functioning.

H. Imahori et al., Chem. Eur. J. 2007, 13, 10182-10193: Effects of Porphyrin Substituents on Film Structure and Photoelectrochemical Properties of Porphyrin/Fullerene Composite Clusters Electrophoretically Deposited on Nanostructured SnO2 Electrodes.

A. Anbarasu et al., Int. J. Biol. Macromolec. 2007, 41, 251-259. Investigations on C-H...pi interactions in RNA binding proteins.

R. P. Saha et al., Proteins 2007, 67, 84-97: Interaction geometry involving planar groups in protein?　protein interfaces.

J. Fantini et al., Biochemistry 2006, 45, 10957-10962: Prediction of glycolipid-binding domains from the amino acid sequence of lipid raft-associated proteins: Applications to HpaA, a protein involved in the adhesion of Helicobacter pylori to gastrointestinal cells.

M. Levy et al., FEBS J. 2006, 273, 5274-5735: The minimal amyloid-forming fragment of the islet amyloid polypeptide is a glycolipid-binding domain.

K. Harata, T. Akiba, Acta Cryst. 2006, D62, 375-38: Structural phase transition of monoclinic crystals of hen egg-white lysozyme.

M. Harigai et al., J. Am. Chem. Soc. 2006, 128, 10646-10647: A single CH/pi weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein.

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

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.

N. Yahi et al., J. Biomed. Sci. 2005, DOI 10.1007/s11373-005-9011-4: Structural analysis of reverse transcriptase mutations at codon 215 explains the predominance of T215Y over T215 in HIV-1 variants selected under antiviral therapy.

Y. Umezawa, M. Nishio, Biopolymers 2005, 79, 248-258: CH/pi hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase. [See page 'Our papers' for Abstract]

C. D. Blundell et al., J. Biol. Chem. 2005, 280, 18189-18201: Towards a structure for a TSG-6 hyaluronan complex by modeling and NMR spectroscopy: insights into other members of the link module superfamily.

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

M. S. Sujatha et al., Biochemistry 2005, 44 , 8554 -8562: Insights into the role of the aromatic residue in galactose-binding sites: MP2/6-311G++** study on galactose- and glucose-aromatic residue analogue complexes.

A. Colette et al., J. Am. Chem. Soc. 2005, 127, 7879-7890: Role for bound water and CH-pi aromatic interactions in photosynthetic electron transfer.

M. Fernandez-Alonso et al., J. Am. Chem. Soc. 2005, 127, 7379-7386: Molecular recognition of saccharides by proteins. Insights on the origin of the carbohydrate-aromatic interactions.

Y. Nakagawa et al., J. Am. Chem. Soc. 2005, 127, 5746-5747: Indolactam-V is involved in the CH/pi interaction with Pro-11 of the PKCd C1B domain: Application for the structural optimization of the PKCd ligand.

J. Vondrasek et al., J. Am. Chem. Soc. 2005, 127, 2615-2619: Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues; Correlated ab initio quantum chemical calculations.

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

M. S. Sujatha et al., Protein Sci. 2004, 13, 2502-2512: Energetics of galactose- and glucose-aromatic amino acid interactions: Implications for binding in galactose-specific proteins. See also M. S. Sujatha, P. V. Balaji, Proteins 2004, 55, 44-65: Identification of common structural features binding sites in galactose-specific proteins.

S. Mohanty et al., J. Mol. Biol. 2004, 337, 434-451: The solution NMR structure of Antheraea polyphemus PBP provides new insight into pheromone recognition by pheromone-binding proteins.

N. Taieb et al., Advanced Drug Delivery Reviews 2004, 56, 779-794: Rafts and related glycosphingolipid-enriched microdomains in the intestinal epithelium: bacterial targets linked to nutrient absorption. [REVIEW]

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

M. M. Babu, Nucleic Acids Res. 2003, 31, 3345-3348: NCI: a server to identify non-canonical interactions in protein structures.

V. Klusak 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.

M. Hayashida et al., J. Mol. Biol. 2003, 334, 551-565: Similarity between portein-protein and protein-carbohydrate interactions, revealed by two crystal structures of lectins from the roots of pokeweed.

R. Bhattacharyya, P. Chakrabarti,J. Mol. Biol. 2003, 331, 925-940: Stereospecific interactions of proline residues in protein structures and complexes.

T. Kinoshita et al., Acta Crystallogr., Sec. D 2003, 59, 299-303: Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside.

M. Muraki, K. Harata, J. Molec. Recogn. 2003, 16, 72-82: X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine.

R. Meurisse et al., Biochem. Biophys. Acta 2003, 36891, 1-12: Aromatic side-chain interactions in proteins. Near- and far-sequence His-X pairs.

H. Dvir et al., Biochemistry 2002, 41, 10810-10818: X-ray structure of Torpedo california acetylcholinesterase complexed with (+)-huperzine A and (-)-huperzine B: Structural evidence for an active site rearrangement.

A. Thomas et al., Proteins 2002, 48, 628-634: Aromatic side-chain interactions in proteins I. Main structural features.

A. Thomas et al., Proteins 2002, 48, 635-644: Aromatic side-chain interactions in proteins II. Near- and far-sequence Phe-X pairs.

M. L. Waters, Curr. Opinion in Chemical Biol. 2002, 6, 736-741: Aromatic interactions in model systems [REVIEW]

D. D. Boehr et al., Chem. & Biol. 2002, 9, 1209-1217: Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3')-IIIa and its nucleotide ligands.

R. Bhattacharyya et al., Protein Eng. 2002, 15, 91-100: Aromatic-aromatic interactions in and around alpha helices.

G. Koellner et al., J. Mol. Biol. 2002, 320, 721-725: A neutral molecule in a cation-binding site: Specific binding of a PEG-SH to acetylcholinesterase from Torpedo california.

F. Zsila et al., Biochem. Pharmacol. 2002, 64, 1651-1660: Retinoic acid binding properties of the lipocalin member beta-lactoglobulin studied by circular dichroism, electronic absorption spectroscopy and molecular modeling method.

A. Lenhart et al., Chemistry & Biology 2002, 9, 639-645: Crystal structure of a squalene cyclase in complex with the potential anticholesteremic drug Ro48-8071.

M. Muraki, Protein and Peptide Lett. 2002, 9, 195-209: The importance of CH/pi interactions to the function of carbohydrate binding proteins. [REVIEW]

T. Kinoshita et al., Acta Crystallogr., Sect. D 2002, 58, 622-626: The structure of human recombinant aldose reductase complexed with the potent inhibitor zenarestat.

R. Bhattacharyya et al., Protein Eng., 2002, 15, 91-100: Aromatic-aromatic interaction in and around alpha-helices.

M. Muraki et al., Biochim. Biophys. Acta 2002, 1569, 10-20: Interactions of wheat-germ agglutinin with GlcNAcbeta1,6Gal sequence.

K. Sakaguchi et al., Peptide Science 2001, 37, 277-280: Destabilization of tumor suppressor protein p53 tetramer by oxidation of Met340.

G. Toth et al., Protein Eng., 2001, 14, 543-547: Stabilization of local structures by pi-CH and aromatic-backbone amide interactions involving prolyl and aromatic residues.

M. S. Weiss et al., Trends in Biochemical Sciences 2001, 26, 521-523: More hydrogen bonds for the (structural) biologist. [REVIEW]

M. Brandi et al., J. Mol. Biol. 2001, 307, 357-377: CH-pi interactions in proteins.

G. Toth et al., Proteins 2001, 47, 373-381: Significance of aromatic-backborn amide interactions in protein structure.

I. Matsui et al., J. Biol. Chem. 2000, 275, 4871-4879: The molecular structure of hyperthermostable aromatic amino transferase with novel substrate specificity from Pirocuccus horikoshii.

Y. Umezawa, M. Nishio, Bioorg. Med. Chem. 2000, 8, 2643-2650: CH/pi interactions in the crystal structure of TATA-box binding protein/DNA complexes. [See page 'Our papers' for Abstract]

A. Robinson et al., Acta Crystallogr., Sect. D 2000, 56, 1376-1384: Structure of the C123S mutant of dienelactone hydrolase (DLH) bound with the PMS moiety of the protease inhibitor phenylmethylsulfonyl fluoride (PMSF).

I. Nakanishi et al., Biopolymers 2000, 53, 434-445: Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastases, at 1.6 A resolution.

M. Muraki et al., Protein Eng. 2000, 13, 385-389: Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin.

P. R. Kumar et al., J. Mol. Biol. 2000, 295, 581-593: The tertiary structure at 1.59 A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti Bainier.

M. Muraki et al., Biochemistry 2000, 39, 292-299: Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.

U. Samanta et al., Proteins 2000, 38, 288-300: Environment of tryptophane side chains in proteins.

D. Pal, P. Chakrabarti, J. Mol. Biol. 1999, 294, 271-288: Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations.

A. Jabs et al., J. Mol. Biol. 1999, 286, 291-304: Non-proline peptide bonds in proteins.

Y. Umezawa, M. Nishio, Bioorg. Med. Chem. 1998, 6, 2507-2515: CH/pi interactions in the crystal structure of class I MHC antigens and their complexes with peptides. [See page 'Our papers' for Abstract]

M. Muraki et al., Acta Crystallogr., Sect. D 1998, 54, 834-843: X-ray structure of human lysozyme labeled with 2',3'-epoxy beta-glycoside of man-beta-1,4-GlcNAc-structural-change and recognition specificity at subsite-B.

Y. Umezawa, M. Nishio, Bioorg. Med. Chem. 1998, 6, 493-504: CH/pi interactions in the crystal structure of guanine-nucleotide binding proteins, src homology-2 domains and human growth hormone in complex with their specific ligands. [See page 'Our papers' for Abstract]

A. Kashima et al., Eur. J. Biochem. 1998, 255, 12-23: X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.

S. E. Zographos et al., Structure 1997, 5, 1413-1425: The structure of glycogen phosphorylase b with an alkyl-dihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor.

J. E. Thompson et al., Biochemistry 1997, 36, 1852-1860: Trihydroxynaphthalene reductase from Magnaporthe grisea: Realization of an active center inhibitor and elucidation of the kinetic mechanism.

K. Harata, M. Muraki, Acta Crystallogr., Sect. D 1997, 53, 650-657: X-ray structure of turkey-egg lysozyme complex with tri-N-acetylchitotriose. Lack of binding ability at subsite A.

M. O'Reilly et al., Nat. Str. Biol. 1997, 4, 405-412: Oligosaccharide substrate binding in Escherchia coli maltodextrin phosphorylase.

M. Nishio et al., Tetrahedron 1995, 51, 8665-8701: The CH/pi interaction: Significance in molecular recognition [REVIEW]. [See page 'Our papers' for Abstract]

M. Nishio et al., Kagaku to Seibutsu 1995, 33, 311-318: CH/pinteractionｪFAn important factor to determine protein specificities [REVIEW]. (in Japanese)

P. Chakrabarti, U. Samanta, J. Mol. Biol. 1995, 251, 9-14: CH/pi interaction in the packing of the adenine ring in protein structures.

K. Takahashi et al., Tetrahedron 1994, 50, 1327-1340: Synthesis and binding of simple neocarzinostatin chromophore analogues to the apoprotein.

M. Hirama J. Synth. Org. Chem. Jpn. 1994, 52, 980-991: Neocarzinostatin complex: Chromophore analogs, binding structure and stabilization mechanism [REVIEW].

W. Hinrichs et al., Science 1994, 264, 418-420: Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance.

T. Tanaka et al., J. Chem. Soc., Chem. Commun. 1993, 1205-1207: Solution structure of the antitumour antibiotic neocarzinostatin, a chromophore-protein complex.

K. H. Kim et al., Science 1993, 262, 1042-1046: Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex.

M. Yun et al., J. Am. Chem. Soc. 1992, 114, 2281-2282: X-ray crystallographic study of covalently modified carboxypeptidase A by 2-benzyl-3,4-epoxybutanoic acid, a pseudomechanism-based inactivator.

M. F. Perutz et al., J. Am. Chem. Soc. 1986, 108, 1064-1078: Hemoglobin as a receptor of drugs and peptides: X-ray studies of the stereochemsitry of binding.

M. Nishio, 29th Symposium on Protein Structures, Osaka, 1978, Abstract, 161-164: CH/pi interaction and the structure of protein. (in Japanese)