@article{MTMT:34199131,
	title = {Amide isomerization pathways: Electronic and structural background of protonation- and deprotonation-mediated cis-trans interconversions},
	url = {https://m2.mtmt.hu/api/publication/34199131},
	author = {Kelemen, Ádám András and Perczel, András and Horváth, Dániel and Jákli, Imre},
	doi = {10.1063/5.0165772},
	journal-iso = {J CHEM PHYS},
	journal = {JOURNAL OF CHEMICAL PHYSICS},
	volume = {159},
	unique-id = {34199131},
	issn = {0021-9606},
	abstract = {The cis-trans isomerization of amide bonds leads to wide range of structural and functional changes in proteins and can easily be the rate-limiting step in folding. The trans isomer is thermodynamically more stable than the cis, nevertheless the cis form can play a role in biopolymers’ function. The molecular system of N-methylacetamide · 2H2O is complex enough to reveal energetics of the cis-trans isomerization at coupled cluster single-double and coupled cluster single–double and perturbative triple [CCSD(T)] levels of theory. The cis-trans isomerization cannot be oversimplified by a rotation along ω, since this rotation is coupled with the N-atom pyramidal inversion, requesting the introduction of a second dihedral angle “α.” Full f(ω,α) potential energy surfaces of the different amide protonation states, critical points and isomerization reaction paths were determined, and the barriers of the neutral, O-protonated and N-deprotonated amides were found too high to allow cis-trans interconversion at room temperature: ∼85, ∼140, and ∼110 kJ mol−1, respectively. For the N-protonated amide bond, the cis form (ω = 0°) is a maximum rather than a minimum, and each ω state is accessible for less than ∼10 kJ mol−1. Here we outline a cis-trans isomerization pathway with a previously undescribed low energy transition state, which suggests that the proton is transferred from the more favorable O- to the N-protonation site with the aid of nearby water molecules, allowing the trans → cis transition to occur at an energy cost of ≤11.6 kJ mol−1. Our results help to explain why isomerase enzymes operate via protonated amide bonds and how N-protonation of the peptide bond occurs via O-protonation.},
	year = {2023},
	eissn = {1089-7690},
	orcid-numbers = {Perczel, András/0000-0003-1252-6416; Horváth, Dániel/0000-0001-8239-3933}
}

@article{MTMT:33307131,
	title = {A carbapenem antibiotic inhibiting a mammalian serine protease: structure of the acylaminoacyl peptidase–meropenem complex},
	url = {https://m2.mtmt.hu/api/publication/33307131},
	author = {Kiss-Szemán, Anna Júlia and Takács, Luca and Orgován, Zoltán and Stráner, Pál and Jákli, Imre and Schlosser, Gitta (Vácziné) and Masiulis, Simonas and Harmat, Veronika and Karancsiné Menyhárd, Dóra and Perczel, András},
	doi = {10.1039/D2SC05520A},
	journal-iso = {CHEM SCI},
	journal = {CHEMICAL SCIENCE},
	volume = {13},
	unique-id = {33307131},
	issn = {2041-6520},
	abstract = {The structure of porcine AAP (pAAP) in a covalently bound complex with meropenem was determined by cryo-EM to 2.1 Å resolution, showing the mammalian serine-protease inhibited by a carbapenem antibiotic.},
	year = {2022},
	eissn = {2041-6539},
	pages = {14264-14276},
	orcid-numbers = {Kiss-Szemán, Anna Júlia/0000-0002-3039-0324; Takács, Luca/0000-0002-4864-8872; Stráner, Pál/0000-0003-2240-8501; Schlosser, Gitta (Vácziné)/0000-0002-7637-7133; Harmat, Veronika/0000-0002-1866-9904; Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:32830377,
	title = {Cryo-EM structure of acylpeptide hydrolase reveals substrate selection by multimerization and a multi-state serine-protease triad},
	url = {https://m2.mtmt.hu/api/publication/32830377},
	author = {Kiss-Szemán, Anna Júlia and Stráner, Pál and Jákli, Imre and Hosogi, Naoki and Harmat, Veronika and Karancsiné Menyhárd, Dóra and Perczel, András},
	doi = {10.1039/D2SC02276A},
	journal-iso = {CHEM SCI},
	journal = {CHEMICAL SCIENCE},
	volume = {13},
	unique-id = {32830377},
	issn = {2041-6520},
	year = {2022},
	eissn = {2041-6539},
	pages = {7132-7142},
	orcid-numbers = {Kiss-Szemán, Anna Júlia/0000-0002-3039-0324; Stráner, Pál/0000-0003-2240-8501; Hosogi, Naoki/0000-0001-6662-1940; Harmat, Veronika/0000-0002-1866-9904; Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:31154881,
	title = {Off-pathway 3D-structure provides protection against spontaneous Asn/Asp isomerization: shielding proteins Achilles heel},
	url = {https://m2.mtmt.hu/api/publication/31154881},
	author = {Láng, András and Jákli, Imre and Enyedi, Kata Nóra and Mező, Gábor and Karancsiné Menyhárd, Dóra and Perczel, András},
	doi = {10.1017/S003358351900009X},
	journal-iso = {Q REV BIOPHYS},
	journal = {QUARTERLY REVIEWS OF BIOPHYSICS},
	volume = {53},
	unique-id = {31154881},
	issn = {0033-5835},
	year = {2020},
	eissn = {1469-8994},
	orcid-numbers = {Láng, András/0000-0002-3329-2359; Enyedi, Kata Nóra/0000-0003-3724-5936; Mező, Gábor/0000-0002-7618-7954; Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Perczel, András/0000-0003-1252-6416}
}

@{MTMT:30805932,
	title = {Elektron- és rezgési spektroszkópia a fehérjekutatásban},
	url = {https://m2.mtmt.hu/api/publication/30805932},
	author = {Farkas, Viktor and Jákli, Imre and Kardos, József and Vass, Elemér},
	booktitle = {Ezerarcú fehérjék},
	unique-id = {30805932},
	year = {2018},
	pages = {277-300},
	orcid-numbers = {Farkas, Viktor/0000-0002-8815-2783; Kardos, József/0000-0002-2135-2932; Vass, Elemér/0000-0001-8898-3846}
}

@article{MTMT:3239373,
	title = {Predictable Conformational Diversity in Foldamers of Sugar Amino Acids},
	url = {https://m2.mtmt.hu/api/publication/3239373},
	author = {Karancsiné Menyhárd, Dóra and Hudaky, I and Jákli, Imre and Juhasz, G and Perczel, András},
	doi = {10.1021/acs.jcim.6b00488},
	journal-iso = {J CHEM INF MODEL},
	journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},
	volume = {57},
	unique-id = {3239373},
	issn = {1549-9596},
	abstract = {A systematic conformational search was carried out for monomers and homohexamers of furanoid beta-amino, acids: cis-(S,R) and trans-(S,S) stereoisomers of aminocyclopentane carboxylic acid (ACPC), two different.aniinofuranuronic acids (AFU(alpha) and AFU(beta)), their isopropylidene derivatives (AFU(ip)), and the key intermediate beta-aminotetrahydrofurancarboxylic acid (ATFC). The stereochemistry of the building blocks was chosen to match that of the natural sugar amino acid (xylose and ribose) precursors (XylAFU and RibAFU). The results show that hexamera of cis-furanoid beta-amino acids show great variability: while hydrophobic.cyclopentane (cis-ACPC)(6) and hydrophilic (XylAFU(alpha/beta))(6) foldamers favor two different zigzagged conformation as hexaMers, the backbone fold turns into a helix in the case of (cis-ATFC)(6) (10 -helix) and (XylAFU(ip))(6) (14 -helix). Trans stereochemistry resulted in hexamers exclusively with the right-handed, helix conformation, (H-12(P))(6), regardless of their polarity. We found that the preferred.oligomeric structure of XylAFU(alpha/beta) is conformationally compatible 'with beta-pleated sheets, while that of the trans/(S,S) units matches with alpha-helices of proteins.},
	keywords = {DERIVATIVES; RECOGNITION; DESIGN; SECONDARY STRUCTURE; BETA-PEPTIDES; HELIX; OLIGOMERS; STRUCTURAL-CHARACTERIZATION; ALPHA/BETA-PEPTIDE FOLDAMERS; GLP-1 RECEPTOR},
	year = {2017},
	eissn = {1549-960X},
	pages = {757-768},
	orcid-numbers = {Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:3229927,
	title = {Four Faces of the Interaction between Ions and Aromatic Rings},
	url = {https://m2.mtmt.hu/api/publication/3229927},
	author = {Papp, Dóra and Petra, Rovó and Jákli, Imre and Császár, Attila Géza and Perczel, András},
	doi = {10.1002/jcc.24816},
	journal-iso = {J COMPUT CHEM},
	journal = {JOURNAL OF COMPUTATIONAL CHEMISTRY},
	volume = {38},
	unique-id = {3229927},
	issn = {0192-8651},
	year = {2017},
	eissn = {1096-987X},
	pages = {1762-1773},
	orcid-numbers = {Császár, Attila Géza/0000-0001-5640-191X; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:3101105,
	title = {Aromatic Cluster Sensor of Protein Folding: Near-UV Electronic Circular Dichroism Bands Assigned to Fold Compactness},
	url = {https://m2.mtmt.hu/api/publication/3101105},
	author = {Farkas, Viktor and Jákli, Imre and Tóth, Gábor and Perczel, András},
	doi = {10.1002/chem.201602455},
	journal-iso = {CHEM-EUR J},
	journal = {CHEMISTRY-A EUROPEAN JOURNAL},
	volume = {22},
	unique-id = {3101105},
	issn = {0947-6539},
	abstract = {Both far- and near-UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222nm reporting secondary structural variations (far-UV range), Lb bands (near-UV range) are applicable as 3D-fold sensors of protein's core structure. In this study we show that both Lb(Tyr) and Lb(Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross-validation, also provided here. The ensemble of 204 ECD spectra of Trp-cage miniproteins is analysed as a training set for "calibrating" Trp↔Tyr folded systems of known NMR structure. While in the far-UV ECD spectra changes are linear as a function of the temperature, near-UV ECD data indicate a non-linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding↔unfolding mechanism. We found that the Lb 293 band is reporting on the 3D-structure compactness. In addition, the pure near-UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85°C) compared to NMR for studying the unfolding of Trp↔Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase-inhibitor etc.) can now be analysed with higher confidence. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
	keywords = {PROTEINS; sensors; Protein Folding; DICHROISM; Structure (composition); Ubiquitin-Protein Ligases; Thermal unfolding; Electronic circular dichroism; Electrochemical sensors; RNA polymerase II; Folding intermediates; Structural variations; Folding propensities; Trp-Tyr interacting residues; Electronic circular dichroism spectra},
	year = {2016},
	eissn = {1521-3765},
	pages = {13871-13883},
	orcid-numbers = {Farkas, Viktor/0000-0002-8815-2783; Tóth, Gábor/0000-0002-3604-4385; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:3091952,
	title = {Hydrogen-Bonding Network Anchors the Cyclic Form of Sugar Arylhydrazones},
	url = {https://m2.mtmt.hu/api/publication/3091952},
	author = {Goldschmidt Gőz, Viktória and Pintér, István and Csámpai, Antal and Jákli, Imre and Zsoldos-Mády, Virág and Perczel, András},
	doi = {10.1002/ejoc.201600462},
	journal-iso = {EUR J ORG CHEM},
	journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY},
	volume = {2016},
	unique-id = {3091952},
	issn = {1434-193X},
	abstract = {The "classical" challenge, raised by Emil Fischer as to why one monosaccharide arylhydrazone adopts a cyclic structure but another an acyclic structure, is answered here. The present comprehensive analysis of hexose and hexosamine arylhydrazones, based on 2D NMR spectroscopy and theoretical modeling, has established that the chain of hydrogen bonds needed for conformational selection can only be completed for d-glucosamine derivatives. Thus, d-glucosamine 4-nitrophenylhydrazone exclusively adopts its cyclic form, but any configurational changes imply the formation of acyclic structures. In conclusion, three criteria dominate structure selection, namely 1) an amino function at the C-2 position, 2) the "all-equatorial" substitution mode of the pyranoid ring, and 3) an electron-withdrawing group on the arylhydrazone are all needed to get the cyclic form only. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},
	keywords = {carbohydrates; hydrazones; conformation analysis; ab initio calculations; Hydrogen bonds},
	year = {2016},
	eissn = {1099-0690},
	pages = {3419-3426},
	orcid-numbers = {Csámpai, Antal/0000-0003-2107-7309; Perczel, András/0000-0003-1252-6416}
}

@article{MTMT:2553691,
	title = {Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide Cα-radical foldamers},
	url = {https://m2.mtmt.hu/api/publication/2553691},
	author = {Gerlei, KZ and Élo, L and Fiser, Béla and Owen, Michael Christopher and Jákli, Imre and Knak, Jensen SJ and Csizmadia, Imre Gyula and Perczel, András and Viskolcz, Béla},
	doi = {10.1016/j.cplett.2013.12.037},
	journal-iso = {CHEM PHYS LETT},
	journal = {CHEMICAL PHYSICS LETTERS},
	volume = {593},
	unique-id = {2553691},
	issn = {0009-2614},
	abstract = {Electron structure calculations on N-acetyl asparagine N-methylamide were performed to identify the global minimum from which radicals were formed after H-abstraction by the OH radical. It was found that the radical generated by breaking the C-H bond of the α-carbon was thermodynamically the most stable one in the gas- and aqueous phases. The extended (βL and βD) backbone conformations are the most stable, but syn-syn or inverse γ-turn (γL) and γ-turn (γ D) have substantial stability too. The highest energy conformers are the degenerate εL and εD foldamers. Clearly, the most stable β foldamer is the most likely intermediate for racemization. © 2013 Elsevier B.V. All rights reserved.},
	keywords = {Free Radicals; amino acids; MODEL PEPTIDES; amphiphiles; OH radical; Most likely; Electron structures; H-abstraction; Energy conformers; Global minima; Aqueous phasis},
	year = {2014},
	eissn = {1873-4448},
	pages = {104-108},
	orcid-numbers = {Fiser, Béla/0000-0003-0603-4626; Perczel, András/0000-0003-1252-6416}
}