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  1. Article ; Online: Hydration effects on Leu's polyproline II population in AcLXPNH₂

    Zhang, Yan / Zhou, Yanjun / He, Liu / Fu, Yu / Wenwen / Hu, Jingjing / Shi, Zhengshuang

    Chemical communications. 2018 May 31, v. 54, no. 45 p.5764-5767

    2018  

    Abstract: Hydration is important in many fundamental processes. To investigate hydration effects on peptide conformations, we examined neighboring-residue and side-chain blocking effects in AcLXPNH₂. A correlation between two effects suggests that hydration ... ...

    Abstract Hydration is important in many fundamental processes. To investigate hydration effects on peptide conformations, we examined neighboring-residue and side-chain blocking effects in AcLXPNH₂. A correlation between two effects suggests that hydration stabilizes PII more than β-structures. Our results are important for understanding the hydration effects on peptide conformations and hydration-forces in general.
    Keywords chemical compounds ; chemical reactions ; peptides ; proline ; reaction mechanisms
    Language English
    Dates of publication 2018-0531
    Size p. 5764-5767.
    Publishing place The Royal Society of Chemistry
    Document type Article ; Online
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c8cc02402b
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  2. Article ; Online: Construction of tunable peptide nucleic acid junctions.

    Duan, Tanghui / He, Liu / Tokura, Yu / Liu, Xin / Wu, Yuzhou / Shi, Zhengshuang

    Chemical communications (Cambridge, England)

    2018  Volume 54, Issue 23, Page(s) 2846–2849

    Abstract: We report here the construction of 3-way and 4-way peptide nucleic acid (PNA) junctions as basic structural units for PNA nanostructuring. The incorporation of amino acid residues into PNA chains makes PNA nanostructures with more structural complexity ... ...

    Abstract We report here the construction of 3-way and 4-way peptide nucleic acid (PNA) junctions as basic structural units for PNA nanostructuring. The incorporation of amino acid residues into PNA chains makes PNA nanostructures with more structural complexity and architectural flexibility possible, as exemplified by building 3-way PNA junctions with tunable nanopores. Given that PNA nanostructures have good thermal and enzymatic stabilities, they are expected to have broad potential applications in biosensing, drug delivery and bioengineering.
    MeSH term(s) Nanostructures/chemistry ; Peptide Nucleic Acids/chemical synthesis ; Peptide Nucleic Acids/chemistry
    Chemical Substances Peptide Nucleic Acids
    Language English
    Publishing date 2018-03-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c8cc00108a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Hydration effects on Leu's polyproline II population in AcLXPNH

    Zhang, Yan / Zhou, Yanjun / He, Liu / Fu, Yu / Zhang, Wenwen / Hu, Jingjing / Shi, Zhengshuang

    Chemical communications (Cambridge, England)

    2018  Volume 54, Issue 45, Page(s) 5764–5767

    Abstract: Hydration is important in many fundamental processes. To investigate hydration effects on peptide conformations, we examined neighboring-residue and side-chain blocking effects in AcLXPNH2. A correlation between two effects suggests that hydration ... ...

    Abstract Hydration is important in many fundamental processes. To investigate hydration effects on peptide conformations, we examined neighboring-residue and side-chain blocking effects in AcLXPNH2. A correlation between two effects suggests that hydration stabilizes PII more than β-structures. Our results are important for understanding the hydration effects on peptide conformations and hydration-forces in general.
    Language English
    Publishing date 2018-05-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/c8cc02402b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities.

    Zhou, Yanjun / He, Liu / Zhang, Wenwen / Hu, Jingjing / Shi, Zhengshuang

    Scientific reports

    2016  Volume 6, Page(s) 27197

    Abstract: Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for ... ...

    Abstract Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides provide vital information. Reliable determination of populations of the α-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH2 and AcGXGNH2 peptides allow us to derive the populations of PII, β and α in AcGXGNH2. Our results show that on average residue X in AcGXGNH2 adopt PII, β, and α 44.7%, 44.5% and 10.8% of time, respectively. The contents of α-conformations for different amino acids define an α-helix nucleation propensity scale. With derived PII, β and α-contents, we can construct a free energy-conformation diagram on each AcGXGNH2 in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.
    Language English
    Publishing date 2016-06-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/srep27197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Ramachandran redux.

    Shi, Zhengshuang / Kallenbach, Neville R

    Proceedings of the National Academy of Sciences of the United States of America

    2010  Volume 108, Issue 1, Page(s) 3–4

    MeSH term(s) Amides/chemistry ; Amides/metabolism ; Hydrogen Bonding ; Models, Molecular ; Protein Conformation ; Protein Folding
    Chemical Substances Amides
    Language English
    Publishing date 2010-12-22
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1017021108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: End effects influence short model peptide conformation.

    He, Liu / Navarro, Abel E / Shi, Zhengshuang / Kallenbach, Neville R

    Journal of the American Chemical Society

    2012  Volume 134, Issue 3, Page(s) 1571–1576

    Abstract: Previously, we derived a P(II) propensity scale using N- and C-terminally blocked host-guest peptide model AcGGXGGNH(2) (X ≠ Gly) and concluded that P(II) represents a dominant conformation in the majority of this series of 19 peptides (Shi et al. Proc. ... ...

    Abstract Previously, we derived a P(II) propensity scale using N- and C-terminally blocked host-guest peptide model AcGGXGGNH(2) (X ≠ Gly) and concluded that P(II) represents a dominant conformation in the majority of this series of 19 peptides (Shi et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17964-17968). Recently, Schweitzer-Stenner and co-workers examined a series of eight short host-guest tripeptides with the sequence GXG (X = A, V, F, S, E, L, M, and K) in which both N- and C-ends were unblocked and reported major differences in P(II) content for F, V, and S compared to our scale (Hagarman et al. J. Am. Chem. Soc. 2010, 132, 540-551). We have investigated four representative amino acids (X = A, V, F, and S) in three series of peptides (GXG, AcGXGNH(2), and AcGGXGGNH(2)) as a function of pH in this study. Our data show that P(II) content in the GXG series (X = A, V, F, and S) is pH-dependent and that the conformations of each amino acid differ markedly between the GXG and AcGXGNH(2)/AcGGXGGNH(2) series. Our results indicate that P(II) scales are sequence and context dependent and the presence of proximal charged end groups exerts a strong effect on P(II) population in short model peptides.
    MeSH term(s) Amino Acid Sequence ; Circular Dichroism ; Hydrogen-Ion Concentration ; Peptides/chemistry ; Protein Conformation
    Chemical Substances Peptides ; polyproline (25191-13-3)
    Language English
    Publishing date 2012-01-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/ja2070363
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: End Effects Influence Short Model Peptide Conformation

    He, Liu / Kallenbach Neville R / Navarro Abel E / Shi Zhengshuang

    Journal of the American Chemical Society. 2012 Jan. 25, v. 134, no. 3

    2012  

    Abstract: Previously, we derived a PII propensity scale using N- and C-terminally blocked host–guest peptide model AcGGXGGNH₂ (X ≠ Gly) and concluded that PII represents a dominant conformation in the majority of this series of 19 peptides (Shi et al. Proc. ... ...

    Abstract Previously, we derived a PII propensity scale using N- and C-terminally blocked host–guest peptide model AcGGXGGNH₂ (X ≠ Gly) and concluded that PII represents a dominant conformation in the majority of this series of 19 peptides (Shi et al. Proc. Natl. Acad. Sci. U.S.A.2005, 102, 17964–17968). Recently, Schweitzer-Stenner and co-workers examined a series of eight short host–guest tripeptides with the sequence GXG (X = A, V, F, S, E, L, M, and K) in which both N- and C-ends were unblocked and reported major differences in PII content for F, V, and S compared to our scale (Hagarman et al. J. Am. Chem. Soc.2010, 132, 540–551). We have investigated four representative amino acids (X = A, V, F, and S) in three series of peptides (GXG, AcGXGNH₂, and AcGGXGGNH₂) as a function of pH in this study. Our data show that PII content in the GXG series (X = A, V, F, and S) is pH-dependent and that the conformations of each amino acid differ markedly between the GXG and AcGXGNH₂/AcGGXGGNH₂ series. Our results indicate that PII scales are sequence and context dependent and the presence of proximal charged end groups exerts a strong effect on PII population in short model peptides.
    Keywords amino acids ; models ; pH ; tripeptides
    Language English
    Dates of publication 2012-0125
    Size p. 1571-1576.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021%2Fja2070363
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  8. Article: Networks for the allosteric control of protein kinases.

    Shi, Zhengshuang / Resing, Katheryn A / Ahn, Natalie G

    Current opinion in structural biology

    2006  Volume 16, Issue 6, Page(s) 686–692

    Abstract: The allosteric regulation of protein kinases serves as an efficient strategy for molecular communication, event coupling and interconversion between catalytic states. Recent co-crystal structures have revealed novel ways in which kinases control activity ...

    Abstract The allosteric regulation of protein kinases serves as an efficient strategy for molecular communication, event coupling and interconversion between catalytic states. Recent co-crystal structures have revealed novel ways in which kinases control activity and substrate specificity following phosphorylation, dimerization, or binding to regulatory proteins, substrates and scaffolds. In addition, hydrogen exchange coupled with mass spectrometry is emerging as a complementary strategy to probe the solution behavior of kinases; recent results have shown that allosteric regulation may involve transitions in protein motions as well as structural rearrangements.
    MeSH term(s) Allosteric Regulation ; Allosteric Site ; Deuterium ; Dimerization ; Extracellular Signal-Regulated MAP Kinases/chemistry ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Hydrogen ; Mass Spectrometry ; Models, Biological ; Models, Molecular ; Protein Kinases/chemistry ; Protein Kinases/metabolism ; Protein Structure, Quaternary ; Signal Transduction
    Chemical Substances Hydrogen (7YNJ3PO35Z) ; Deuterium (AR09D82C7G) ; Protein Kinases (EC 2.7.-) ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24)
    Language English
    Publishing date 2006-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1068353-7
    ISSN 0959-440X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2006.10.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3206: Show issues Location:
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  9. Article: New reverse micelle surfactant systems optimized for high-resolution NMR spectroscopy of encapsulated proteins.

    Shi, Zhengshuang / Peterson, Ronald W / Wand, A Joshua

    Langmuir : the ACS journal of surfaces and colloids

    2005  Volume 21, Issue 23, Page(s) 10632–10637

    Abstract: Sodium bis(2-ethylhexyl)sulfosuccinate (AOT) is a surfactant commonly used to encapsulate water soluble proteins within the aqueous core of a reverse micelle. In the context of high-resolution NMR studies of encapsulated proteins the size of the ... ...

    Abstract Sodium bis(2-ethylhexyl)sulfosuccinate (AOT) is a surfactant commonly used to encapsulate water soluble proteins within the aqueous core of a reverse micelle. In the context of high-resolution NMR studies of encapsulated proteins the size of the resulting reverse micelle is critically important. We have designed and synthesized a short AOT analogue, 3,3-dimethyl-1-butylsulfosuccinate sodium salt and determined that it is able to form reverse micelles and to encapsulate the protein ubiquitin with high structural fidelity. AOT is often found to significantly destabilize encapsulated proteins, largely through charge-charge interactions between the anionic headgroup and the surface of the protein. Here we demonstrate, for the first time, that proportional mixtures of anionic and cationic surfactants can form reverse micelles that are also capable of protein encapsulation with high fidelity.
    MeSH term(s) Cations ; Magnetic Resonance Spectroscopy/methods ; Micelles ; Proteins/chemistry ; Surface-Active Agents/chemistry
    Chemical Substances Cations ; Micelles ; Proteins ; Surface-Active Agents
    Language English
    Publishing date 2005-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/la051409a
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  10. Article: Conformation of the backbone in unfolded proteins.

    Shi, Zhengshuang / Chen, Kang / Liu, Zhigang / Kallenbach, Neville R

    Chemical reviews

    2006  Volume 106, Issue 5, Page(s) 1877–1897

    MeSH term(s) Alanine ; Kinetics ; Models, Molecular ; Molecular Conformation ; Proline ; Protein Conformation ; Protein Folding ; Proteins/chemistry ; Thermodynamics
    Chemical Substances Proteins ; Proline (9DLQ4CIU6V) ; Alanine (OF5P57N2ZX)
    Language English
    Publishing date 2006-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 207949-5
    ISSN 1520-6890 ; 0009-2665
    ISSN (online) 1520-6890
    ISSN 0009-2665
    DOI 10.1021/cr040433a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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