1
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Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Pappone F, Grillo A, Nakashio M, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Inaba T, Tanino Y, Nukui Y, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions. ACS Infect Dis 2023; 9:2226-2251. [PMID: 37850869 PMCID: PMC10644350 DOI: 10.1021/acsinfecdis.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 10/19/2023]
Abstract
The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream of highly contagious and antibody-resistant strains, which in turn led to classifying Omicron as a variant of concern. We systematically collected Raman spectra from six Omicron subvariants available in Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, and BA.2.75) and applied machine-learning algorithms to decrypt their structural characteristics at the molecular scale. Unique Raman fingerprints of sulfur-containing amino acid rotamers, RNA purines and pyrimidines, tyrosine phenol ring configurations, and secondary protein structures clearly differentiated the six Omicron subvariants. These spectral characteristics, which were linked to infectiousness, transmissibility, and propensity for immune evasion, revealed evolutionary motifs to be compared with the outputs of genomic studies. The availability of a Raman "metabolomic snapshot", which was then translated into a barcode to enable a prompt subvariant identification, opened the way to rationalize in real-time SARS-CoV-2 activity and variability. As a proof of concept, we applied the Raman barcode procedure to a nasal swab sample retrieved from a SARS-CoV-2 patient and identified its Omicron subvariant by coupling a commercially available magnetic bead technology with our newly developed Raman analyses.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Molecular Science and Nanosystems, Ca’
Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Eriko Ohgitani
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Hayata Imamura
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Pappone
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Alfio Grillo
- Department
of Mathematical Science, Politecnico di
Torino, Corso Duca degli
Abruzzi 24, 10129 Torino, Italy
| | - Maiko Nakashio
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Masaharu Shin-Ya
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Toshiro Yamamoto
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
- Department
of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic
Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Tohru Inaba
- Department
of Infection Control & Laboratory Medicine, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Tanino
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yoko Nukui
- Department of Clinical Laboratory, University
Hospital, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
| | - Koichiro Higasa
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Yoshiki Yasukochi
- Genome Analysis, Institute of Biomedical
Science, Kansai Medical University, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Kazu Okuma
- Department
of Microbiology, Kansai Medical University,
School of Medicine, 2-5-1
Shinmachi, Hirakata 573-1010, Osaka Prefecture, Japan
| | - Osam Mazda
- Department
of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
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2
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Pezzotti G, Adachi T, Imamura H, Bristol DR, Adachi K, Yamamoto T, Kanamura N, Marin E, Zhu W, Kawai T, Mazda O, Kariu T, Waku T, Nichols FC, Riello P, Rizzolio F, Limongi T, Okuma K. In Situ Raman Study of Neurodegenerated Human Neuroblastoma Cells Exposed to Outer-Membrane Vesicles Isolated from Porphyromonas gingivalis. Int J Mol Sci 2023; 24:13351. [PMID: 37686157 PMCID: PMC10488263 DOI: 10.3390/ijms241713351] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to elucidate the chemistry of cellular degeneration in human neuroblastoma cells upon exposure to outer-membrane vesicles (OMVs) produced by Porphyromonas gingivalis (Pg) oral bacteria by monitoring their metabolomic evolution using in situ Raman spectroscopy. Pg-OMVs are a key factor in Alzheimer's disease (AD) pathogenesis, as they act as efficient vectors for the delivery of toxins promoting neuronal damage. However, the chemical mechanisms underlying the direct impact of Pg-OMVs on cell metabolites at the molecular scale still remain conspicuously unclear. A widely used in vitro model employing neuroblastoma SH-SY5Y cells (a sub-line of the SK-N-SH cell line) was spectroscopically analyzed in situ before and 6 h after Pg-OMV contamination. Concurrently, Raman characterizations were also performed on isolated Pg-OMVs, which included phosphorylated dihydroceramide (PDHC) lipids and lipopolysaccharide (LPS), the latter in turn being contaminated with a highly pathogenic class of cysteine proteases, a key factor in neuronal cell degradation. Raman characterizations located lipopolysaccharide fingerprints in the vesicle structure and unveiled so far unproved aspects of the chemistry behind protein degradation induced by Pg-OMV contamination of SH-SY5Y cells. The observed alterations of cells' Raman profiles were then discussed in view of key factors including the formation of amyloid β (Aβ) plaques and hyperphosphorylated Tau neurofibrillary tangles, and the formation of cholesterol agglomerates that exacerbate AD pathologies.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Davide Redolfi Bristol
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Keiji Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (K.A.); (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (H.I.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, 3301 College Avenue, Fort Lauderdale, FL 33314, USA;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.A.); (O.M.)
| | - Toru Kariu
- Department of Life Science, Shokei University, Chuo-ku, Kuhonji, Kumamoto 862-8678, Japan;
| | - Tomonori Waku
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan;
| | - Frank C. Nichols
- Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, University of Connecticut, 263 Farmington Avenue, Storrs, CT 06030, USA;
| | - Pietro Riello
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Flavio Rizzolio
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (P.R.); (F.R.)
| | - Tania Limongi
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129 Torino, Italy;
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
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3
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Pezzotti G, Ohgitani E, Ikegami S, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Okuma K, Mazda O. Instantaneous Inactivation of Herpes Simplex Virus by Silicon Nitride Bioceramics. Int J Mol Sci 2023; 24:12657. [PMID: 37628838 PMCID: PMC10454075 DOI: 10.3390/ijms241612657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Hydrolytic reactions taking place at the surface of a silicon nitride (Si3N4) bioceramic were found to induce instantaneous inactivation of Human herpesvirus 1 (HHV-1, also known as Herpes simplex virus 1 or HSV-1). Si3N4 is a non-oxide ceramic compound with strong antibacterial and antiviral properties that has been proven safe for human cells. HSV-1 is a double-stranded DNA virus that infects a variety of host tissues through a lytic and latent cycle. Real-time reverse transcription (RT)-polymerase chain reaction (PCR) tests of HSV-1 DNA after instantaneous contact with Si3N4 showed that ammonia and its nitrogen radical byproducts, produced upon Si3N4 hydrolysis, directly reacted with viral proteins and fragmented the virus DNA, irreversibly damaging its structure. A comparison carried out upon testing HSV-1 against ZrO2 particles under identical experimental conditions showed a significantly weaker (but not null) antiviral effect, which was attributed to oxygen radical influence. The results of this study extend the effectiveness of Si3N4's antiviral properties beyond their previously proven efficacy against a large variety of single-stranded enveloped and non-enveloped RNA viruses. Possible applications include the development of antiviral creams or gels and oral rinses to exploit an extremely efficient, localized, and instantaneous viral reduction by means of a safe and more effective alternative to conventional antiviral creams. Upon incorporating a minor fraction of micrometric Si3N4 particles into polymeric matrices, antiherpetic devices could be fabricated, which would effectively impede viral reactivation and enable high local effectiveness for extended periods of time.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (S.I.); (W.Z.)
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.Y.); (N.K.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Department of Molecular Science and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.)
| | - Saki Ikegami
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (S.I.); (W.Z.)
| | - Masaharu Shin-Ya
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.)
| | - Tetsuya Adachi
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.Y.); (N.K.)
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.Y.); (N.K.)
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.Y.); (N.K.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (S.I.); (W.Z.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan; (T.Y.); (N.K.)
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (S.I.); (W.Z.)
| | - Kazu Okuma
- Department of Microbiology, School of Medicine, Kansai Medical University, 2-5-1 Shinmachi, Hirakata 573-1010, Japan;
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan; (E.O.); (M.S.-Y.); (T.A.)
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4
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Casier R, Duhamel J. Synergetic Effects of Alanine and Glycine in Blob-Based Methods for Predicting Protein Folding Times. J Phys Chem B 2023; 127:1325-1337. [PMID: 36749707 DOI: 10.1021/acs.jpcb.2c08155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The polypeptide PGlyAlaGlu was prepared with 20 mol % glycine (Gly), 36 mol % d,l-alanine (Ala), and 44 mol % d,l-glutamic acid (Glu) and labeled with the dye 1-pyrenemethylamine to yield a series of Py-PGlyAlaGlu samples. The fluorescence decays of the Py-PGlyAlaGlu samples were analyzed according to the fluorescence blob model (FBM) to obtain the number Nblobexp of amino acids (aa's) encompassed inside the subvolume Vblob of the polypeptide probed by an excited pyrene. An Nblobexp value of 29 (±2) was retrieved for Py-PGlyAlaGlu, which was much larger than for any of the copolypeptide PGlyGlu or PAlaGlu prepared with either Gly and Glu or Ala and Glu, respectively. The continuous increase in Nblobexp with decreasing side chain size (SCS) from 10 aa's for PGlu to 16 aa's for PAlaGlu and 22 aa's for PGlyGlu was used earlier to define the reach of an aa and determine the groups of aa's that could interact with each other along a polypeptide backbone according to their SCS. These groups of aa's, referred to as blobs, led to the implementation of blob-based models (BBM) to predict the folding time τFtheo,BBM of 145 proteins, which was found to match their experimental folding time τFexp with a relatively high 0.71 correlation coefficient. Nevertheless, the much higher Nblobexp value found for Py-PGlyAlaGlu compared to all other pyrene-labeled polypeptides studied to date indicates that the reach of aa's along a polypeptide sequence is affected not only by SCS but also by synergetic effects between different aa's. Following this new insight, a revised BBM was implemented to predict τFtheo,BBM for 195 proteins assuming the existence or absence of synergies to control the interactions between aa's along a polypeptide sequence. Similarly good correlation coefficients of 0.71 and 0.74 were obtained for a direct 1:1 comparison of τFexp and τFtheo,BBM for the 195 proteins without and with synergies, respectively. This result suggests that synergetic effects between different aa's have little effect on τFtheo,BBM predicted from BBM underlying the robustness of this methodology.
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Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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5
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O'Neill N, Lima TA, Ferreira FF, Thursch L, Alvarez N, Schweitzer-Stenner R. Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine. J Phys Chem B 2022; 126:8080-8093. [PMID: 36194765 DOI: 10.1021/acs.jpcb.2c05010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 106 Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P212121 space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States.,Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Thamires A Lima
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Fabio Furlan Ferreira
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Av. Dos Estados, 5001, S622-3, Santo André, São Paulo09210-580, Brazil
| | - Lavenia Thursch
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Nicolas Alvarez
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
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6
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Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Nishimura I, Mazda O. Raman Fingerprints of the SARS-CoV-2 Delta Variant and Mechanisms of Its Instantaneous Inactivation by Silicon Nitride Bioceramics. ACS Infect Dis 2022; 8:1563-1581. [PMID: 35819780 PMCID: PMC9305655 DOI: 10.1021/acsinfecdis.2c00200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 02/06/2023]
Abstract
Raman spectroscopy uncovered molecular scale markers of the viral structure of the SARS-CoV-2 Delta variant and related viral inactivation mechanisms at the biological interface with silicon nitride (Si3N4) bioceramics. A comparison of Raman spectra collected on the TY11-927 variant (lineage B.1.617.2; simply referred to as the Delta variant henceforth) with those of the JPN/TY/WK-521 variant (lineage B.1.617.1; referred to as the Kappa variant or simply as the Japanese isolate henceforth) revealed the occurrence of key mutations of the spike receptor together with profound structural differences in the molecular structure/symmetry of sulfur-containing amino acid and altered hydrophobic interactions of the tyrosine residue. Additionally, different vibrational fractions of RNA purines and pyrimidines and dissimilar protein secondary structures were also recorded. Despite mutations, hydrolytic reactions at the surface of silicon nitride (Si3N4) bioceramics induced instantaneous inactivation of the Delta variant at the same rate as that of the Kappa variant. Contact between virions and micrometric Si3N4 particles yielded post-translational deimination of arginine spike residues, methionine sulfoxidation, tyrosine nitration, and oxidation of RNA purines to form formamidopyrimidines. Si3N4 bioceramics proved to be a safe and effective inorganic compound for instantaneous environmental sanitation.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo
Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, 160-0023 Tokyo,
Japan
- Center for Advanced Medical Engineering and
Informatics, Osaka University, 2-2 Yamadaoka, Suita, Osaka
565-0854, Japan
- Institute of Biomaterials and Bioengineering,
Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai,
Chiyoda-ku, Tokyo 101-0062, Japan
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
- Biomedical Research Center, Kyoto Institute
of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Eriko Ohgitani
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
| | - Yuki Fujita
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Hayata Imamura
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Masaharu Shin-Ya
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
- Department of Dental Medicine, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto
Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585,
Japan
| | - Ichiro Nishimura
- Division of Advanced Prosthodontics, The Jane and
Jerry Weintraub Center for Reconstructive Biotechnology, UCLA School of
Dentistry, Los Angeles, California 90095, United
States
| | - Osam Mazda
- Department of Immunology, Graduate School of Medical
Science, Kyoto Prefectural University of Medicine, Kamigyo-ku,
465 Kajii-cho, Kyoto 602-8566, Japan
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7
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Pezzotti G, Boschetto F, Ohgitani E, Fujita Y, Shin‐Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Nishimura I, Mazda O. Raman Molecular Fingerprints of SARS-CoV-2 British Variant and the Concept of Raman Barcode. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103287. [PMID: 34877818 PMCID: PMC8787433 DOI: 10.1002/advs.202103287] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/04/2021] [Indexed: 06/12/2023]
Abstract
The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub-types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK-521), and found bold vibrational differences. These included: i) fractions of sulfur-containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
- Department of Orthopedic SurgeryTokyo Medical University6‐7‐1 Nishi‐Shinjuku, Shinjuku‐kuTokyo160‐0023Japan
- The Center for Advanced Medical Engineering and InformaticsOsaka University2‐2 Yamadaoka, SuitaOsaka565‐0854Japan
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University2‐3‐10 Kanda‐Surugadai, Chiyoda‐kuTokyo101‐0062Japan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Francesco Boschetto
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Eriko Ohgitani
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Yuki Fujita
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
| | - Masaharu Shin‐Ya
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Tetsuya Adachi
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Toshiro Yamamoto
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Narisato Kanamura
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Elia Marin
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Wenliang Zhu
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
| | - Ichiro Nishimura
- Division of Advanced ProsthodonticsThe Jane and Jerry Weintraub Center for Reconstructive BiotechnologyUCLA School of DentistryLos AngelesCA90095USA
| | - Osam Mazda
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
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8
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Glycine in Water Favors the Polyproline II State. Biomolecules 2020; 10:biom10081121. [PMID: 32751224 PMCID: PMC7463814 DOI: 10.3390/biom10081121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.
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9
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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10
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Edwards-Gayle CC, Castelletto V, Hamley IW, Barrett G, Greco F, Hermida-Merino D, Rambo RP, Seitsonen J, Ruokolainen J. Self-Assembly, Antimicrobial Activity, and Membrane Interactions of Arginine-Capped Peptide Bola-Amphiphiles. ACS APPLIED BIO MATERIALS 2019; 2:2208-2218. [PMID: 31157325 PMCID: PMC6537463 DOI: 10.1021/acsabm.9b00172] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/16/2019] [Indexed: 12/27/2022]
Abstract
The self-assembly and antimicrobial activity of two novel arginine-capped bola-amphiphile peptides, namely RA6R and RA9R (R, arginine; A, alanine) are investigated. RA6R does not self-assemble in water due to its high solubility, but RA9R self-assembles above a critical aggregation concentration into ordered nanofibers due to the high hydrophobicity of the A9block. The structure of the RA9R nanofibers is studied by cryogenic transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). Circular dichroism spectroscopy shows that both RA6R and RA9R adopt coil conformations in water at low concentration, but only RA9R adopts a β-sheet conformation at high concentration. SAXS and differential scanning calorimetry are used to study RA6R and RA9R interactions with a mixed lipid membrane that models a bacterial cell wall, consisting of multilamellar 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol/1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine vesicles. Cytotoxicity studies show that RA6R is more cytocompatible than RA9R. RA6R has enhanced activity against the Gram-negative pathogen P. aeruginosa at a concentration where viability of mammalian cells is retained. RA9R has little antimicrobial activity, independently of concentration. Our results highlight the influence of the interplay between relative charge and hydrophobicity on the self-assembly, cytocompatibility, and bioactivity of peptide bola-amphiphiles.
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Affiliation(s)
- Charlotte
J. C. Edwards-Gayle
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire OX11 0DE, U.K.
| | - Valeria Castelletto
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Ian W. Hamley
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | - Glyn Barrett
- School
of Biological Sciences, University of Reading, Reading RG6 6UR, U.K.
| | - Francesca Greco
- School
of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, U.K.
| | | | - Robert P. Rambo
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire OX11 0DE, U.K.
| | - Jani Seitsonen
- Department
of Applied Physics, Aalto School of Science, P.O. Box 15100, FI-00076 Aalto, Finland
| | - Janne Ruokolainen
- Department
of Applied Physics, Aalto School of Science, P.O. Box 15100, FI-00076 Aalto, Finland
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11
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Koyambo-Konzapa SJ, Dhaouadi Z, Nsangou M. Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method. J Mol Graph Model 2019; 88:194-202. [DOI: 10.1016/j.jmgm.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022]
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12
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Yadav NS, Choudhury D. Conformational perturbation of peptides in presence of polar organic solvents. J Mol Graph Model 2019; 89:1-12. [PMID: 30831385 DOI: 10.1016/j.jmgm.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/08/2019] [Accepted: 02/20/2019] [Indexed: 11/17/2022]
Abstract
The critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the addition of polar organic solvents have important consequences for the conformation of these molecules. However, experimental studies of such perturbations often report different kinds of effects depending on the solvent used and/or the sequence/structure of the molecule under study. In this work we report a simulation based comparative study on the effects of adding two common organic solvents viz. Dimethyl sulfoxide (DMSO) and Acetonitrile (MeCN) on the dynamical conformation of a test peptide Ace-Gly-X-Gly-Nme where X is any amino acid. Our studies identify important differences in peptide solvation by these two solvents, which we attempt to correlate with the kinetic stability of the conformation, as well as the identity of the central 'X' residue in the test peptide.
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Affiliation(s)
- Neetu Singh Yadav
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Devapriya Choudhury
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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13
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Jakubek RS, White SE, Asher SA. UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide. J Phys Chem B 2019; 123:1749-1763. [PMID: 30717595 DOI: 10.1021/acs.jpcb.8b10783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D2Q20K2 (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.
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14
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Castelletto V, Barnes RH, Karatzas KA, Edwards-Gayle CJC, Greco F, Hamley IW, Seitsonen J, Ruokolainen J. Restructuring of Lipid Membranes by an Arginine-Capped Peptide Bolaamphiphile. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1302-1311. [PMID: 30056711 DOI: 10.1021/acs.langmuir.8b01014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We study the self-assembly of arginine-capped bolaamphiphile peptide RA3R (A: alanine, R: arginine) together with its binding to model membranes and its cytotoxicity and antimicrobial activity. Anionic 2-oleoyl-1-palmitoyl- sn-glycero-3-phospho-rac-(1-glycerol) sodium salt/2-oleoyl-1-palmitoyl- sn-glycero-3-phosphoethanolamine (POPG/POPE) vesicles and zwitterionic 1,2-dioleoyl- sn-glycero-3-phosphocholine/2-oleoyl-1-palmitoyl- sn-glycero-3-phosphocholine (POPC/DOPC) vesicles are used as model membranes to mimic bacterial and mammalian cell membranes, respectively. We show that RA3R adopts a polyproline-II collagen-like conformation in water. Binding of RA3R to POPG/POPE vesicles induces a strong correlation between the lipid bilayers, driven by RA3R/POPG attractive electrostatic interaction together with a shift of the intramolecular POPE zwitterionic interaction toward an attractive electrostatic interaction with the RA3R. Populations of RA3R/POPG/POPE vesicles comprise different bilayer spacings, dA and dB, controlled by the conformation of the lipid chains corresponding to the Lβ (gel-like) and Lα (liquid-crystal) phases, respectively. Cryo-TEM images reveal the presence of vesicles with no internal structure, compartmentalized thin-wall vesicles, or multilayer vesicles with uncorrelated layers and compartmentalization depending on the RA3R/POPG/POPE composition. In contrast, the interaction of RA3R with multilamellar POPC/DOPC vesicles leads to the decorrelation of the lipid bilayers. RA3R was tolerated by skin fibroblast cells for a concentration up to 0.01 wt %, while 0.25 wt % RA3R proved to be an efficient antibacterial agent against Gram-positive bacteria L. monocytogenes. Our results highlight the ability of RA3R to distinguish between bacterial and mammalian cells and establish this peptide as a candidate to reduce the proliferation of L. monocytogenes bacteria.
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Affiliation(s)
- Valeria Castelletto
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Ruth H Barnes
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Kimon-Andreas Karatzas
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Charlotte J C Edwards-Gayle
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Francesca Greco
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Ian W Hamley
- School of Chemistry, Food Biosciences and Pharmacy , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Jani Seitsonen
- Department of Applied Physics , Aalto School of Science , P.O. Box 15100, FI-00076 Aalto , Finland
| | - Janne Ruokolainen
- Department of Applied Physics , Aalto School of Science , P.O. Box 15100, FI-00076 Aalto , Finland
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15
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Wei C, Pohorille A. Sequence-Dependent Interfacial Adsorption and Permeation of Dipeptides across Phospholipid Membranes. J Phys Chem B 2017; 121:9859-9867. [PMID: 28982244 DOI: 10.1021/acs.jpcb.7b08238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We investigate permeation of three blocked dipeptides with different side chain polarity across a phospholipid membrane and their behavior at the water-membrane interface by way of molecular dynamics simulations. Hydrophilic serine-serine dipeptide is found to desorb from the interface to aqueous phase, whereas hydrophobic phenylalanine-leucine and amphiphilic serine-leucine tend to accumulate at the interface with a free energy minimum of -3 kcal/mol. All three dipeptides exhibit free energy barriers to permeation across the membrane located at the center of the bilayer. The height of the barrier is strongly sequence dependent and increases with the dipeptide polarity. It is equal to 3.5, 6.4, and 10.0 kcal/mol for phenylalanine-leucine, serine-leucine, and serine-serine, respectively. The corresponding permeability coefficients are equal to 4.6 × 10-3, 4.5 × 10-5, and 8.7 × 10-8 cm/s. The apparent insensitivity of membrane permeability to hydrophobicity of dipeptides, found in some experiments, is attributed to neglecting corrections for unstirred water layers near membrane surface, which are significant for hydrophobic species. Different hydrophobicity of the dipeptides also influences their conformations and orientations, both at the interface and inside the membrane. In particular, penetration of hydrophilic serine-serine dipeptide causes the formation of water-filled defects in the bilayer. These results are relevant to the delivery of peptide-based therapeutic agents.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94143, United States
| | - Andrew Pohorille
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, California 94035, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94143, United States
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16
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DiGuiseppi D, Milorey B, Lewis G, Kubatova N, Farrell S, Schwalbe H, Schweitzer-Stenner R. Probing the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycylalanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy. J Phys Chem B 2017; 121:5744-5758. [DOI: 10.1021/acs.jpcb.7b02899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Nina Kubatova
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
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17
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Milorey B, Farrell S, Toal SE, Schweitzer-Stenner R. Demixing of water and ethanol causes conformational redistribution and gelation of the cationic GAG tripeptide. Chem Commun (Camb) 2016; 51:16498-501. [PMID: 26414527 DOI: 10.1039/c5cc06097d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The cationic tripeptide GAG undergoes three conformational changes in binary mixtures of water and ethanol. At 17 mol% of ethanol conformational sampling is shifted from pPII towards β-strands. A more pronounced shift in the same direction occurs at 40 mol%. At ca. 55 mol% of ethanol and above a peptide concentration of ca. 0.2 M the ternary peptide-water-ethanol mixture forms a hydrogel which is comprised of unusually large crystalline like non-β sheet fibrils forming a sample spanning matrix.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, USA.
| | - Stefanie Farrell
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, USA.
| | - Siobhan E Toal
- Department of Chemistry, University of Pennsylvania, 231, South 34th-Street, Philadelphia, PA 19104, USA
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18
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Ilawe NV, Raeber AE, Schweitzer-Stenner R, Toal SE, Wong BM. Assessing backbone solvation effects in the conformational propensities of amino acid residues in unfolded peptides. Phys Chem Chem Phys 2016; 17:24917-24. [PMID: 26343224 DOI: 10.1039/c5cp03646a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Conformational ensembles of individual amino acid residues within model GxG peptides (x representing different amino acid residues) are dominated by a mixture of polyproline II (pPII) and β-strand like conformations. We recently discovered rather substantial differences between the enthalpic and entropic contributions to this equilibrium for different amino acid residues. Isoleucine and valine exceed all other amino acid residues in terms of their rather large enthalpic stabilization and entropic destabilization of polyproline II. In order to shed light on these underlying physical mechanisms, we performed high-level DFT calculations to explore the energetics of four representative GxG peptides where x = alanine (A), leucine (L), valine (V), and isoleucine (I) in explicit water (10 H2O molecules with a polarizable continuum water model) and in vacuo. We found that the large energetic contributions to the stabilization of pPII result, to a major extent, from peptide-water, water-water interactions, and changes of the solvent self-energy. Differences between the peptide-solvent interaction energies of hydration in pPII and β-strand peptides are particularly important for the pPII ⇌ β equilibria of the more aliphatic peptides GIG and GLG. Furthermore, we performed a vibrational analysis of the four peptides in both conformations and discovered a rather substantial mixing between water motions and peptide vibrations below 700 cm(-1). We found that the respective vibrational entropies are substantially different for the considered conformations, and their contributions to the Gibbs/Helmholtz energy stabilize β-strand conformations. Taken together, our results underscore the notion of the solvent being the predominant determinant of peptide (and protein) conformations in the unfolded state.
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Affiliation(s)
- Niranjan V Ilawe
- Department of Chemical & Environmental Engineering, and Materials Science & Engineering Program, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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19
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Meral D, Toal S, Schweitzer-Stenner R, Urbanc B. Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study. J Phys Chem B 2015; 119:13237-51. [PMID: 26418575 DOI: 10.1021/acs.jpcb.5b06281] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid residues of unfolded peptides in water sample only a few basins in the Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics of guest residues, X, in GXG peptides in water were recently reported to be dominated by pPII and β-strand-like (β) conformations, resulting in an enthalpy-entropy compensation at ∼300 K. Using molecular dynamics (MD) in explicit solvent, we here examine pPII and β conformational ensembles of 15 guest residues in GXG peptides, quantify local orientation of water around their side chains through novel water orientation plots, and study their hydration and hydrogen bonding properties. We show that pPII and β ensembles are characterized by distinct water orientations: pPII ensembles are associated with an increased population of water oriented in parallel to the side chain surface whereas β ensembles exhibit more heterogeneous water orientations. The backbone hydration is significantly higher in pPII than in β ensembles. Importantly, pPII to β hydration differences and the solvent accessible surface area of Cβ hydrogens both correlate with experimental pPII propensities. We propose that pPII conformations are stabilized by a local, hydrogen-bonded clathrate-like water structure and that residue-specific intrinsic pPII propensities reflect distinct abilities of side chains to template this water structure.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Siobhan Toal
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | | | - Brigita Urbanc
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States.,Faculty of Mathematics and Physics, University of Ljubljana , 1000 Ljubljana, Slovenia
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20
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Toal S, Schweitzer-Stenner R. Local order in the unfolded state: conformational biases and nearest neighbor interactions. Biomolecules 2014; 4:725-73. [PMID: 25062017 PMCID: PMC4192670 DOI: 10.3390/biom4030725] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 12/23/2022] Open
Abstract
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.
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Affiliation(s)
- Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19026, USA.
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21
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Candelaresi M, Ragnoni E, Cappelli C, Corozzi A, Lima M, Monti S, Mennucci B, Nuti F, Papini AM, Foggi P. Conformational analysis of Gly-Ala-NHMe in D(2)O and DMSO solutions: a two-dimensional infrared spectroscopy study. J Phys Chem B 2013; 117:14226-37. [PMID: 24164089 DOI: 10.1021/jp406139t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A relevant number of experiments on short peptides has been performed in recent years. One of the major problems rises from the simultaneous presence of slightly different conformers at equilibrium in solution. In the present paper, the conformational characteristics of the Gly-l-Ala-Methyl amide dipeptide in D2O and DMSO solutions are investigated by nonlinear IR spectroscopy. The pump-probe scheme with ultrashort mid-infrared pulses, in the Amide I region, is used to determine the mutual orientation of the two C═O bonds and the dynamics due to solute-solvent interactions. The coupling between Amide I modes is evaluated from both linear and 2D spectra. The interconversion between the different conformations occurs on time scales longer than the vibrational lifetime, and the spectral diffusion observed in 2D spectra is attributed to the solvent dynamics. Quantum mechanical calculations and molecular dynamics simulations are performed to identify the most stable geometries. By comparing the experimental and the theoretical data, we establish the prevalence of β-like polar conformers in both water and DMSO solvents.
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Affiliation(s)
- Marco Candelaresi
- Heriot-Watt University, Edinburgh Campus , Edinburgh, Scotland EH14 4AS
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22
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Jiang F, Han W, Wu YD. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development. Phys Chem Chem Phys 2013; 15:3413-28. [PMID: 23385383 DOI: 10.1039/c2cp43633g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The local conformational (φ, ψ, χ) preferences of amino acid residues remain an active research area, which are important for the development of protein force fields. In this perspective article, we first summarize spectroscopic studies of alanine-based short peptides in aqueous solution. While most studies indicate a preference for the P(II) conformation in the unfolded state over α and β conformations, significant variations are also observed. A statistical analysis from various coil libraries of high-resolution protein structures is then summarized, which gives a more coherent view of the local conformational features. The φ, ψ, χ distributions of the 20 amino acids have been obtained from a protein coil library, considering both backbone and side-chain conformational preferences. The intrinsic side-chain χ(1) rotamer preference and χ(1)-dependent Ramachandran plot can be generally understood by combining the interaction of the side-chain Cγ/Oγ atom with two neighboring backbone peptide groups. Current all-atom force fields such as AMBER ff99sb-ILDN, ff03 and OPLS-AA/L do not reproduce these distributions well. A method has been developed by combining the φ, ψ plot of alanine with the influence of side-chain χ(1) rotamers to derive the local conformational features of various amino acids. It has been further applied to improve the OPLS-AA force field. The modified force field (OPLS-AA/C) reproduces experimental (3)J coupling constants for various short peptides quite well. It also better reproduces the temperature-dependence of the helix-coil transition for alanine-based peptides. The new force field can fold a series of peptides and proteins with various secondary structures to their experimental structures. MD simulations of several globular proteins using the improved force field give significantly less deviation (RMSD) to experimental structures. The results indicate that the local conformational features from coil libraries are valuable for the development of balanced protein force fields.
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Affiliation(s)
- Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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23
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Toal S, Meral D, Verbaro D, Urbanc B, Schweitzer-Stenner R. pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. J Phys Chem B 2013; 117:3689-706. [PMID: 23448349 DOI: 10.1021/jp310466b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.
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Affiliation(s)
- Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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24
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Schweitzer-Stenner R, Hagarman A, Toal S, Mathieu D, Schwalbe H. Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. I. Tripeptides with long and predominantly hydrophobic side chains. Proteins 2013; 81:955-67. [PMID: 23229832 DOI: 10.1002/prot.24225] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 11/10/2022]
Abstract
We performed a conformational analysis of the central residues of three tripeptides glycyl-L-isoleucyl-glycine (GIG), glycyl-L-tyrosyl-glycine (GYG) and glycyl-L-arginyl-glycine (GRG) in aqueous solution, based on a global analysis of amide I' band profiles and NMR J-coupling constants. The results are compared with recently reported distributions of GVG, GFG and GEG. For GIG and GYG, we found that even though the polyproline II (pPII) fraction is below 0.5, it is still the most populated conformation, whereas GVG and GFG show both a larger β-strand fraction. For GRG, we observed a clear dominance of pPII over β-strand, reminiscent of observations for GEG and GKG. This finding indicates that terminal charges on otherwise hydrophobic residue side chains stabilize pPII over β-strand conformations. For all peptides investigated we found that a variety of compact and turn-like conformations constitute nearly 20 percent of their conformational distributions. Attempts to analyze our data with a simple two-state pPII-->/<--β model therefore do not yield any satisfactory reproduction of experimental results. A comparison of the obtained GxG ensembles with conformational distributions of GxG segments in truncated coil libraries (helices and sheets omitted) revealed a much larger fraction of type II β(i+2) and type III β like conformations for the latter. Thus, a comparison of conformational distributions of unfolded peptide segments in solution and in coil libraries reveal interesting information on how the interplay between intrinsic propensities of amino acid residues and non-local interactions in polypeptide chains determine the conformations of loop segments in proteins.
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25
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Verbaro DJ, Mathieu D, Toal SE, Schwalbe H, Schweitzer-Stenner R. Ionized Trilysine: A Model System for Understanding the Nonrandom Structure of Poly-l-lysine and Lysine-Containing Motifs in Proteins. J Phys Chem B 2012; 116:8084-94. [DOI: 10.1021/jp303794s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel J. Verbaro
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Daniel Mathieu
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Siobhan E. Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Harald Schwalbe
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
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26
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Duitch L, Toal S, Measey TJ, Schweitzer-Stenner R. Triaspartate: A Model System for Conformationally Flexible DDD Motifs in Proteins. J Phys Chem B 2012; 116:5160-71. [DOI: 10.1021/jp2121565] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Duitch
- Department of Chemistry, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Thomas J. Measey
- Department of Chemistry, University of Pennsylvania, Philadelphia,
Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
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27
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Han C, Wang J. Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides. Chemphyschem 2012; 13:1522-34. [DOI: 10.1002/cphc.201100995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/09/2022]
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28
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Setnička V, Hlaváček J, Urbanová M. Oligopeptide-porphyrin interactions studied by circular dichroism spectroscopy: the effect of metalloporphyrin axial ligands on peptide matrix conformation. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424608000650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vibrational (VCD) and electronic circular dichroism (ECD) spectroscopies were used to investigate non-covalent interactions between the cationic tripeptide L-lysyl-L-alanyl-L-alanine (KAA) and the anionic porphyrin meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) in aqueous solution. Also studied were the interactions between KAA and the three metal derivatives of TPPS (copper(II), iron(III), and manganese(III)), each of which has a different number of axial ligands. VCD spectra in the amide I' ( C = O stretching vibration) region are extremely sensitive to peptide conformation, and, consequently, provide direct information about the conformational changes of host oligopeptide matrices caused by electrostatic interaction with guest porphyrin molecules. We found that pure KAA adopts a left-handed polyproline II (PPII) helical conformation when dissolved in aqueous solution at near-neutral pH values. When mixed with metal-free TPPS under the same conditions, VCD intensities were markedly reduced in the amide I' region and a new negative band was observed at 1634 cm−1; both findings indicating the transition of the PPII conformation into a less compact structure having similarities to β-sheet, herein termed a β-sheet-like conformation. In the case of the metal derivatives of TPPS studied, only variations in the VCD intensities in the amide I' region were observed. Compared to the results for pure KAA, the binding of Cu (II) TPPS , which has no axial ligand, resulted in the greatest decrease in amide I' VCD intensity. Nevertheless, the shape of a VCD spectrum characteristic for a PPII conformation was maintained, thereby indicating the presence of an “extended” PPII conformation in the Cu (II) TPPS -KAA complex. Conversely, Mn (III) TPPS , which has two axial ligands, did not significantly affect the PPII conformation of KAA in the Mn (III) TPPS -KAA complex. The effects of the metalation and axial ligation of TPPS on the conformation of KAA in peptide-porphyrin complexes are discussed, together with the results of our ECD study.
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Affiliation(s)
- Vladimír Setnička
- Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
| | - Jan Hlaváček
- Department of Natural Products, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, Prague 6, 166 10, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Technická 5, Prague 6, 166 28, Czech Republic
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29
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Schweitzer-Stenner R, Soffer JB, Verbaro D. Structure analysis of unfolded peptides I: vibrational circular dichroism spectroscopy. Methods Mol Biol 2012; 895:271-313. [PMID: 22760325 DOI: 10.1007/978-1-61779-927-3_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).
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30
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Li W, Qin M, Tie Z, Wang W. Effects of solvents on the intrinsic propensity of peptide backbone conformations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041933. [PMID: 22181201 DOI: 10.1103/physreve.84.041933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/16/2011] [Indexed: 05/31/2023]
Abstract
We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.
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Affiliation(s)
- Wenfei Li
- National Laboratory of Solid State Microstructure, and Department of Physics, Nanjing University, Nanjing 210093, China
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31
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Toal S, Amidi O, Schweitzer-Stenner R. Conformational Changes of Trialanine Induced by Direct Interactions between Alanine Residues and Alcohols in Binary Mixtures of Water with Glycerol and Ethanol. J Am Chem Soc 2011; 133:12728-39. [DOI: 10.1021/ja204123g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Siobhan Toal
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Omid Amidi
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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32
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Volkov VV, Chelli R, Muniz-Miranda F, Righini R. Structural Properties of a Membrane Associated Anchor Dipeptide. J Phys Chem B 2011; 115:5294-303. [DOI: 10.1021/jp109284z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Victor V. Volkov
- European Laboratory for Nonlinear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- European Laboratory for Nonlinear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Francesco Muniz-Miranda
- European Laboratory for Nonlinear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Roberto Righini
- European Laboratory for Nonlinear Spectroscopy (LENS), Università di Firenze, Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica “Ugo Schiff”, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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33
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Zhang R, Wu WJ. Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/05/504-508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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Oh KI, Kim W, Joo C, Yoo DG, Han H, Hwang GS, Cho M. Azido Gauche Effect on the Backbone Conformation of β-Azidoalanine Peptides. J Phys Chem B 2010; 114:13021-9. [DOI: 10.1021/jp107359m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Woosung Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Cheonik Joo
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Dong-Geun Yoo
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Geum-Sook Hwang
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea, and Korea Basic Science Institute, Seoul 136-713, Korea
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35
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Jiang F, Han W, Wu YD. Influence of side chain conformations on local conformational features of amino acids and implication for force field development. J Phys Chem B 2010; 114:5840-50. [PMID: 20392111 DOI: 10.1021/jp909088e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Statistical analysis of coil regions in protein structures has been used to obtain the local backbone phi, psi preferences of amino acids, which agree well with the NMR experiments of unfolded peptides and proteins. We analyzed the conformational features of amino acid residues in a restricted coil library of 4220 high-resolution protein crystal structures. In addition to Gly, Ala, and Pro, the phi, psi distribution (Ramachandran plot) of each amino acid is analyzed with respect to three side chain conformers: g+ (chi(1) approximately -60 degrees), g- (chi(1) approximately 60 degrees), and t (chi(1) approximately 180 degrees). The statistical study indicates that the effect of side chain conformations on phi, psi distributions is even greater than the effect of amino acid types. On the basis of the chi(1), phi, psi conformational preferences, the amino acids in addition to Gly, Pro, and Ala can be divided into five types: (1) ordinary amino acids, (2) Ser, (3) Asp and Asn, (4) Val and Ile, and (5) Thr, each with distinguished chi(1) rotamers. The alpha-helix, beta-sheet, and type-I beta-turn preferences of the different rotamers of various amino acid types can be captured by their intrinsic phi, psi preferences from our coil library. Molecular dynamics simulations of dipeptide Ac-X-NHMe and tetrapeptide Ac-A-X-A-NHMe models give nearly the same side chain rotamer distributions. However, for many amino acids, both OPLS-AA/L and AMBER-FF03 force fields give very different chi(1) rotamer distributions from the coil library. This may partially explain why dipeptide models sometimes cannot reproduce those of protein structures well. The current coil library analysis may be valuable in improving the force field for protein simulations.
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Affiliation(s)
- Fan Jiang
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
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36
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Pizzanelli S, Forte C, Monti S, Zandomeneghi G, Hagarman A, Measey TJ, Schweitzer-Stenner R. Conformations of phenylalanine in the tripeptides AFA and GFG probed by combining MD simulations with NMR, FTIR, polarized Raman, and VCD spectroscopy. J Phys Chem B 2010; 114:3965-78. [PMID: 20184301 DOI: 10.1021/jp907502n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Conformational properties of small, flexible peptides are a matter of ongoing interest since they can be considered as models for unfolded proteins. However, the investigation of the conformations of small peptides is challenging as they are ensembles of rapidly interconverting conformers; moreover, the different methods used are prone to different approximations and errors. In order to obtain more reliable results, it is prudent to combine different techniques; here, molecular dynamics (MD) simulations together with nuclear magnetic resonance (NMR), Fourier transform IR (FTIR), polarized Raman, and vibrational circular dichroism (VCD) measurements were used to study the conformational propensity of phenylalanine in the tripeptides AFA and GFG, motivated by the relevance of phenylalanine for the self-aggregation of peptides. The results of this analysis indicate that the F residue predominantly populates the beta-strand (beta) and polyproline II (PPII) conformations in both AFA and GFG. However, while phenylalanine exhibits a propensity for beta-strand conformations in GFG (0.40 < or = beta population < or = 0.69 and 0.29 < or = PPII population < or = 0.42), the substitution of terminal glycines with alanine residues induces a higher population of PPII (0.31 < or = beta population < or = 0.50 and 0.37 < or = PPII population < or = 0.57).
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Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, via G. Moruzzi, 1 56124 Pisa, Italy.
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37
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Gaigeot MP. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. Phys Chem Chem Phys 2010; 12:10198-209. [PMID: 20539891 DOI: 10.1039/c003485a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université d'Evry val d'Essonne, LAMBE UMR8587 Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Blvd F. Mitterrand, Bât. Maupertuis, 91025 Evry, France.
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38
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Hagarman A, Measey TJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants. J Am Chem Soc 2010; 132:540-51. [PMID: 20014772 DOI: 10.1021/ja9058052] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A reliable intrinsic propensity scale of amino acid residues is indispensable for an assessment of how local conformational distributions in the unfolded state can affect the folding of peptides and proteins. Short host-guest peptides, such as GxG tripeptides, are suitable tools for probing such propensities. To explore the conformational distributions sampled by the central amino acid residue in these motifs, we combined vibrational (IR, Raman, and VCD) with NMR spectroscopy. The data were analyzed in terms of a superposition of two-dimensional Gaussian distribution functions in the Ramachandran space pertaining to subensembles of polyproline II, beta-strand, right- and left-handed helical, and gamma-turn-like conformations. The intrinsic propensities of eight amino acid residues (x = A, V, F, L, S, E, K, and M) in GxG peptides were determined as mole fractions of these subensembles. Our results show that alanine adopts primarily (approximately 80%) a PPII-like conformation, while valine and phenylalanine were found to sample PPII and beta-strand-like conformations equally. The centers of the respective beta-strand distributions generally do not coincide with canonical values of dihedral angles of residues in parallel or antiparallel beta-strands. In fact, the distributions for most residues found in the beta-region significantly overlap the PPII-region. A comparison with earlier reported results for trivaline reveals that the terminal valines increase the beta-strand propensity of the central valine residue even further. Of the remaining investigated amino acids, methionine preferred PPII the most (0.64), and E, S, L, and K exhibit moderate (0.56-0.45) PPII propensities. Residues V, F, S, E, and L sample, to a significant extent, a region between the canonical PPII and (antiparallel) beta-strand conformations. This region coincides with the sampling reported for L and V using theoretical predictions (Tran et al. Biochemistry 2005, 44, 11369). The distributions of all investigated residues differ from coil library and computationally predicted distributions in that they do not exhibit a substantial sampling of helical conformations. We conclude that this sampling of helical conformations arises from the context dependence, for example, neighboring residues, in proteins and longer peptides, some of which is long-range.
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Affiliation(s)
- Andrew Hagarman
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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Schweitzer-Stenner R. Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. J Phys Chem B 2009; 113:2922-32. [PMID: 19243204 DOI: 10.1021/jp8087644] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The conformational preference of individual amino acid residues in the unfolded state of peptides and proteins is the subject of a continuous debate. Research has mostly been focused on alanine, owing to its abundance in proteins and its relevance for the understanding of helix <----> coil transitions. In the current study, we have analyzed the amide I band profiles of the IR, isotropic and anisotropic Raman, and VCD profiles of trialanine in terms of a conformational model which, for the first time, explicitly considers the entire ensemble of possible conformations rather than representative structures. The distribution function utilized for a satisfactory simulation of the amide I band profiles was found to also reproduce a set of five J coupling constants reported by Graf et al. (Graf, J.; et al. J. Am. Chem. Soc. 2007, 129, 1179). The results of our analysis reveal a PPII fraction of approximately 0.84 for the central alanine residue, which strongly corroborates the notion that alanine has a very high PPII propensity, exceeding the values obtained from restricted coil libraries. We performed a similar analysis for trivaline and found that the dominant fraction of its central residue is a beta-strand. The fraction of the respective distribution is 0.68. The remaining fraction contains contributions from helical and PPII conformations. The results of our analysis enable us to decide on the suitability of force fields used for MD simulations of short alanine-containing peptides. The paper establishes vibrational spectroscopy as a suitable method to explore the energy landscape of amino acid residues.
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Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32nd and Chestnut Streets, Philadelphia, Pennsylvania 19104, USA.
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Setnička V, Hlaváček J, Urbanová M. Cationic oligopeptides with the repeating sequence L-lysyl-L-alanyl-L-alanine: conformational and thermal stability study using optical spectroscopic methods. J Pept Sci 2009; 15:533-9. [DOI: 10.1002/psc.1154] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fedorov MV, Goodman JM, Kolombet VV, Schumm S, Socorro IM. Conformational changes of trialanine in sodium halide solutions: An in silico study. J Mol Liq 2009. [DOI: 10.1016/j.molliq.2008.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abramavicius D, Palmieri B, Voronine DV, Šanda F, Mukamel S. Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives. Chem Rev 2009; 109:2350-408. [PMID: 19432416 PMCID: PMC2975548 DOI: 10.1021/cr800268n] [Citation(s) in RCA: 321] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kwac K, Lee KK, Han JB, Oh KI, Cho M. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. J Chem Phys 2008; 128:105106. [PMID: 18345930 DOI: 10.1063/1.2837461] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.
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Affiliation(s)
- Kijeong Kwac
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Cao Y, Xiang TX, Anderson BD. Development of Structure−Lipid Bilayer Permeability Relationships for Peptide-like Small Organic Molecules. Mol Pharm 2008; 5:371-88. [DOI: 10.1021/mp700100n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yichen Cao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Tian-Xiang Xiang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
| | - Bradley D. Anderson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536
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Grdadolnik J, Grdadolnik SG, Avbelj F. Determination of conformational preferences of dipeptides using vibrational spectroscopy. J Phys Chem B 2008; 112:2712-8. [PMID: 18260662 DOI: 10.1021/jp7096313] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The NMR coupling constants ((3)J(H(N), H(alpha))) of dipeptides indicate that the backbone conformational preferences vary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denatured proteins, and the coil regions of native proteins. Detailed characterization of the conformational preferences of dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here, we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. The main advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, which enables the determination of the conformational preferences of short-lived states. Accuracy of structure determination using vibrational spectroscopy depends critically on identification of the vibrational parameters that are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the (3)J(H(N), H(alpha)). These two infrared vibrational parameters are thus analogous to (3)J(H(N), H(alpha)), indicators for the preference for the dihedral angle phi. We also show that the intensities of the components of the amide III bands in infrared spectra and the intensities of the skeletal vibrations in Raman spectra are indicators of populations of the P(II), beta, and alpha(R) conformations. The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the beta conformation increases in valine dipeptides. The populations of the alpha(R) conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.
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Affiliation(s)
- Joze Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia.
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Sheu SY, Schlag EW, Selzle HL, Yang DY. Molecular Dynamics of Hydrogen Bonds in Protein−D2O: The Solvent Isotope Effect. J Phys Chem A 2008; 112:797-802. [DOI: 10.1021/jp0771668] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - E. W. Schlag
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - H. L. Selzle
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
| | - Dah-Yen Yang
- Department of Life Sciences, National Yang-Ming University, Taipei 112, Taiwan, Institute für Physikalische und Theoretische Chemie, TU-München, Lichtenbergstrasse 4, 85748 Garching, Germany, and Institute of Atomic and Molecular Science, Academia Sinica, Taipei 106, Taiwan
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Kim E, Jang S, Pak Y. Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation. J Chem Phys 2008; 127:145104. [PMID: 17935448 DOI: 10.1063/1.2775450] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.
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Affiliation(s)
- Eunae Kim
- Department of Chemistry, Pusan National University, Busan 609-735, Korea
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Morozov AN, Lin SH. Modeling of folding and unfolding mechanisms in alanine-based alpha-helical polypeptides. J Phys Chem B 2007; 110:20555-61. [PMID: 17034243 DOI: 10.1021/jp061781e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
alpha-Helix formation is known to be opposed by the entropy loss due to the folding and favored by the energy of molecular interactions. However, the underlying mechanism of these factors is still being discussed. Here we have used the experimental and calculation data for short alanine-based peptides embedded in water to model the mechanism of helix folding and unfolding and to calculate microscopically the free energy factors of alanine in the frame of helix coil conformational integrals. Classical helix-coil transition theories take into account the interactions in a peptide chain only if the i, i + 3 peptide bond participates in hydrogen bonding. But quantum mechanical calculations showed that interactions of the i, i + 2 peptide bond play an important role in helix folding too. We also included the short-range repulsive interactions due to molecular steric clashes and the end effects due to polar/hydrogen-bonding interactions at the N and C termini. The helix and coil regions of peptide conformational space were defined using an experimental steric criterion for hydrogen bonding. Arginine helix propensity was discussed and estimated. Monte Carlo numerical simulations of thermodynamics and kinetics for the 21 amino acid alpha-helical polypeptide Ac-A5(AAARA)3A-NMe were carried out and found to be in an agreement with the experimental results.
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Affiliation(s)
- Alexander N Morozov
- Institute of Atomic and Molecular Sciences, Academia Sinica, PO Box 23-166, Taipei, Taiwan, Republic of China.
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Jalkanen KJ, Degtyarenko IM, Nieminen RM, Cao X, Nafie LA, Zhu F, Barron LD. Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0361-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abramavicius D, Mukamel S. Chirality-induced signals in coherent multidimensional spectroscopy of excitons. J Chem Phys 2007; 124:034113. [PMID: 16438573 DOI: 10.1063/1.2104527] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nonlocal second- and third-order susceptibilities of an isotropic ensemble of aggregates are calculated by solving the nonlinear exciton equations which map the system into coupled anharmonic oscillators. Both electric and magnetic contributions are included using the minimal-coupling Hamiltonian. The various tensor components are evaluated to first order in the optical wave vector k. Additional structural information about the interchromophore distances, which is not accessible through zeroth-order contributions (the dipole approximation), is contained to the first order in k. New resonant second- and third-order signals predicted for chiral molecules provide multidimensional extensions of circular dichroism spectroscopy. Numerical simulations demonstrate the sensitivity of third-order signals to the secondary structural motiffs of peptides.
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Affiliation(s)
- Darius Abramavicius
- Theoretical Physics Department, Faculty of Physics of Vilnius University, Sauletekio Avenue 9, Building 3, 10222 Vilnius, Lithuania
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