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  1. Article ; Online: Ion Recognition beyond Size Matching: Cooperative Hydration Effect on the K

    Hirata, Keisuke / Sato, Eiko / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    The journal of physical chemistry letters

    2023  Volume 14, Issue 24, Page(s) 5567–5572

    Abstract: The naturally occurring ionophore valinomycin (VM) selectively transports K ...

    Abstract The naturally occurring ionophore valinomycin (VM) selectively transports K
    Language English
    Publishing date 2023-06-12
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A bottom-up approach to the ion recognition mechanism of K

    Suzuki, Yukina / Hirata, Keisuke / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 35, Page(s) 20803–20812

    Abstract: K ...

    Abstract K
    MeSH term(s) Alkalies ; Coordination Complexes ; Ions/chemistry ; Lasers ; Metals, Alkali/chemistry ; Peptides ; Spectrum Analysis ; Water/chemistry
    Chemical Substances Alkalies ; Coordination Complexes ; Ions ; Metals, Alkali ; Peptides ; Water (059QF0KO0R)
    Language English
    Publishing date 2022-09-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d2cp01667b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Potassium and sodium ion complexes with a partial peptide of the selectivity filter in K

    Negoro, Takumi / Hirata, Keisuke / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    Physical chemistry chemical physics : PCCP

    2021  Volume 23, Issue 21, Page(s) 12045–12050

    Abstract: ... of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water ... Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks ... significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule ...

    Abstract Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks Na+. The presence of water in the SF during ion translocation remains under debate due to the experimental and computational challenges in characterizing the interactions between water, ions, and the SF. Our bottom-up approach has been applied to a system composed of a partial peptide of the SF (Ac-tyrosine-NHMe) with a metal ion and a single water molecule to probe these interactions. The IR photodissociation spectra of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water molecule binding sites are ion-dependent. In addition, the ion-peptide distances are elongated significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule. This striking structural difference with the water molecule is discussed in relation to ion selectivity and translocation within the K+ channel.
    Language English
    Publishing date 2021-06-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d1cp00936b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Double Ion Trap Laser Spectroscopy of Alkali Metal Ion Complexes with a Partial Peptide of the Selectivity Filter in K

    Suzuki, Yukina / Hirata, Keisuke / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    The journal of physical chemistry. A

    2021  Volume 125, Issue 44, Page(s) 9609–9618

    Abstract: Potassium ion channels selectively permeate K ...

    Abstract Potassium ion channels selectively permeate K
    MeSH term(s) Alkalies ; Coordination Complexes ; Ions ; Lasers ; Metals, Alkali ; Peptides ; Spectrophotometry, Infrared ; Temperature
    Chemical Substances Alkalies ; Coordination Complexes ; Ions ; Metals, Alkali ; Peptides
    Language English
    Publishing date 2021-10-12
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.1c06440
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Rethinking Ion Transport by Ionophores: Experimental and Computational Investigation of Single Water Hydration in Valinomycin-K

    Sato, Eiko / Hirata, Keisuke / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    The journal of physical chemistry letters

    2021  Volume 12, Issue 6, Page(s) 1754–1758

    Abstract: Valinomycin is a macrocyclic ionophore that transports K ...

    Abstract Valinomycin is a macrocyclic ionophore that transports K
    MeSH term(s) Computational Chemistry ; Hydrophobic and Hydrophilic Interactions ; Ion Transport ; Ionophores/chemistry ; Potassium/chemistry ; Spectrometry, Mass, Electrospray Ionization/methods ; Spectrophotometry, Infrared/methods ; Valinomycin/chemistry ; Water/chemistry
    Chemical Substances Ionophores ; Water (059QF0KO0R) ; Valinomycin (2001-95-8) ; Potassium (RWP5GA015D)
    Language English
    Publishing date 2021-02-11
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.0c03372
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Alkali and Alkaline Earth Metal Ions Complexes with a Partial Peptide of the Selectivity Filter in K

    Otsuka, Remina / Hirata, Keisuke / Sasaki, Yuta / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2020  Volume 21, Issue 8, Page(s) 687

    Abstract: ... shows the efficacy of a bottom-up approach to ion selectivity of K ...

    Abstract The front cover artwork is provided by Takashi Tsujino (Science Graphics Co., Ltd.) . The image shows the efficacy of a bottom-up approach to ion selectivity of K
    Language English
    Publishing date 2020-04-20
    Publishing country Germany
    Document type Journal Article
    ISSN 1439-7641
    ISSN (online) 1439-7641
    DOI 10.1002/cphc.202000246
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Alkali and Alkaline Earth Metal Ions Complexes with a Partial Peptide of the Selectivity Filter in K

    Otsuka, Remina / Hirata, Keisuke / Sasaki, Yuta / Lisy, James M / Ishiuchi, Shun-Ichi / Fujii, Masaaki

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2020  Volume 21, Issue 8, Page(s) 712–724

    Abstract: ... in the KcsA K ...

    Abstract The infrared (IR) spectra of alkali and alkaline earth metal ion complexes with the Ac-Tyr-NHMe (GYG) peptide have been measured by laser photodissociation in a cold ion trap coupled with an electrospray mass spectrometer. The GYG peptide corresponds to a portion of the ion selectivity filter in the KcsA K
    Language English
    Publishing date 2020-03-11
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1439-7641
    ISSN (online) 1439-7641
    DOI 10.1002/cphc.202000033
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Ion-peptide interactions between alkali metal ions and a termini-protected dipeptide: modeling a portion of the selectivity filter in K

    Ishiuchi, Shun-Ichi / Sasaki, Yuta / Lisy, James M / Fujii, Masaaki

    Physical chemistry chemical physics : PCCP

    2018  Volume 21, Issue 2, Page(s) 561–571

    Abstract: ... step in characterizing these interactions, the structures of Na+ and K+ complexed to the Ac-Tyr-NHMe ... chains comprising the selectivity filter of a K+ channel. This peptide contains two carbonyl groups ...

    Abstract Potassium channels have the unique ability to allow the selective passage of potassium ions at near diffusion-free rates while inhibiting the passage of more abundant sodium ions. Local interactions between chemical functional groups and the ions are responsible for both selectivity and transport. As an initial step in characterizing these interactions, the structures of Na+ and K+ complexed to the Ac-Tyr-NHMe peptide have been determined from infrared laser spectroscopy and supporting ab initio calculations. Ac-Tyr-NHMe, a termini-protected peptide sequence, replicates the GYG portion of one of the four peptide chains comprising the selectivity filter of a K+ channel. This peptide contains two carbonyl groups, among the eight C[double bond, length as m-dash]O groups forming the S1 binding site of the selectivity filter. Three conformations have been identified for both ions by laser IR-IR double resonance methods. Two conformations have the ion bound to the two C[double bond, length as m-dash]O groups. The third conformation has, in addition, a cation-π interaction with the aromatic ring of tyrosine, i.e. tridentate binding. The relative contributions of the three conformers are approximately the same for K+Ac-Tyr-NHMe, while the tridentate conformer is preferred for Na+Ac-Tyr-NHMe. These differences will be discussed in the context of ion mobility and selectivity.
    MeSH term(s) Ions/chemistry ; Metals, Alkali/chemistry ; Models, Molecular ; Peptides/chemistry ; Potassium Channels/chemistry ; Potassium Channels/metabolism
    Chemical Substances Ions ; Metals, Alkali ; Peptides ; Potassium Channels
    Language English
    Publishing date 2018-10-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c8cp05839c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Influence of hydration on ion-biomolecule interactions: M(+)(indole)(H2O)(n) (M = Na, K; n = 3-6).

    Ke, Haochen / Lisy, James M

    Physical chemistry chemical physics : PCCP

    2015  Volume 17, Issue 38, Page(s) 25354–25364

    Abstract: ... cation-water-indole bridging interactions were observed. The different charge densities of Na(+) and K ... insights into the Na(+)/K(+)(indole)(H2O)3-6 cluster ion complexes. Isotopic (H/D) analyses were applied ...

    Abstract The indole functional group can be found in many biologically relevant molecules, such as neurotransmitters, pineal hormones and medicines. Indole has been used as a tractable model to study the hydration structures of biomolecules as well as the interplay of non-covalent interactions within ion-biomolecule-water complexes, which largely determine their structure and dynamics. With three potential binding sites: above the six- or five-member ring, and the N-H group, the competition between π and hydrogen bond interactions involves multiple locations. Electrostatic interactions from monovalent cations are in direct competition with hydrogen bonding interactions, as structural configurations involving both direct cation-indole interactions and cation-water-indole bridging interactions were observed. The different charge densities of Na(+) and K(+) give rise to different structural conformers at the same level of hydration. Infrared spectra with parallel hybrid functional-based calculations and Gibbs free energy calculations revealed rich structural insights into the Na(+)/K(+)(indole)(H2O)3-6 cluster ion complexes. Isotopic (H/D) analyses were applied to decouple the spectral features originating from the OH and NH stretches. Results showed no evidence of direct interaction between water and the NH group of indole (via a σ-hydrogen bond) at current levels of hydration with the incorporation of cations. Hydrogen bonding to a π-system, however, was ubiquitous at hydration levels between two and five.
    MeSH term(s) Hydrogen Bonding ; Indoles/chemistry ; Ions/chemistry ; Potassium/chemistry ; Sodium/chemistry ; Water/chemistry
    Chemical Substances Indoles ; Ions ; Water (059QF0KO0R) ; indole (8724FJW4M5) ; Sodium (9NEZ333N27) ; Potassium (RWP5GA015D)
    Language English
    Publishing date 2015-10-14
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c5cp01565k
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Modeling the CH Stretch Vibrational Spectroscopy of M(+)[Cyclohexane] (M = Li, Na, and K) Ions.

    Sibert, Edwin L / Tabor, Daniel P / Lisy, James M

    The journal of physical chemistry. A

    2015  Volume 119, Issue 41, Page(s) 10293–10299

    Abstract: The CH stretch vibrations of M(+)[cyclohexane][Ar] (M = Li, Na, and K) cluster ions were ... theoretically modeled. Results were compared to the corresponding infrared photodissociation spectra of Patwari and Lisy ...

    Abstract The CH stretch vibrations of M(+)[cyclohexane][Ar] (M = Li, Na, and K) cluster ions were theoretically modeled. Results were compared to the corresponding infrared photodissociation spectra of Patwari and Lisy [ J. Chem. Phys A 2007 , 111 , 7585 ]. The experimental spectra feature a substantial spread in CH stretch vibration frequencies due to the alkali metal cation binding to select hydrogens of cyclohexane. This spread was observed to increase with decreasing metal ion size. Exploring the potential energy landscape revealed the presence of three conformers whose energy minima lie within ∼1 kcal of each other. It was determined that in all conformers the metal ion interacts with three hydrogen atoms; these hydrogen atoms can be either equatorial or axial. The corresponding spectra for these conformers were obtained with a theoretical model Hamiltonian [ J. Chem. Phys. 2013 , 138 , 064308 ] that consists of local mode CH stretches bilinearly coupled to each other and Fermi coupled to lower frequency modes. Frequencies and coupling parameters were obtained from electronic structure calculations that were subsequently scaled on the basis of previous studies. Theoretical spectra of a single low energy conformer were found to match well with the experimental spectra. The relative frequency shifts with changing metal ion size were accurately modeled with parameters generated by using ωB97X-D/6-311++(2d,p) calculations.
    Language English
    Publishing date 2015-10-15
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.5b07461
    Database MEDical Literature Analysis and Retrieval System OnLINE

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