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Journal articles on the topic 'Hydrogen Bond Surrogate'

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Author: Grafiati

Published: 6 September 2023

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1

Sawyer, Nicholas, and Paramjit S. Arora. "Hydrogen Bond Surrogate Stabilization of β-Hairpins." ACS Chemical Biology 13, no. 8 (July 13, 2018): 2027–32. http://dx.doi.org/10.1021/acschembio.8b00641.

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2

Joy, Stephen T., and Paramjit S. Arora. "An optimal hydrogen-bond surrogate for α-helices." Chemical Communications 52, no. 33 (2016): 5738–41. http://dx.doi.org/10.1039/c6cc01104g.

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3

Reddy, Sravanthi S., Sunit Pal, Sudip Ghosh, and Erode N. Prabhakaran. "Hydrogen Bond Surrogate‐Constrained Dynamic Antiparallel β‐Sheets." ChemBioChem 22, no. 12 (May 20, 2021): 2111–15. http://dx.doi.org/10.1002/cbic.202100028.

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4

Sawyer, Nicholas, and Paramjit S. Arora. "Using Hydrogen Bond Surrogate Technology to Stabilize Beta-Hairpins." Biophysical Journal 112, no. 3 (February 2017): 177a. http://dx.doi.org/10.1016/j.bpj.2016.11.979.

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5

Dimartino, Gianluca, Deyun Wang, Ross N. Chapman, and Paramjit S. Arora. "Solid-Phase Synthesis of Hydrogen-Bond Surrogate-Derived α-Helices." Organic Letters 7, no. 12 (June 2005): 2389–92. http://dx.doi.org/10.1021/ol0506516.

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6

Miller, Stephen E., Neville R. Kallenbach, and Paramjit S. Arora. "Reversible α-helix formation controlled by a hydrogen bond surrogate." Tetrahedron 68, no. 23 (June 2012): 4434–37. http://dx.doi.org/10.1016/j.tet.2011.12.068.

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7

Wang, Deyun, Kang Chen, Gianluca Dimartino, and Paramjit S. Arora. "Nucleation and stability of hydrogen-bond surrogate-based α-helices." Org. Biomol. Chem. 4, no. 22 (2006): 4074–81. http://dx.doi.org/10.1039/b612891b.

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8

Sawyer, Nicholas, and Paramjit S. Arora. "Hydrogen Bond Surrogate Beta-Hairpins to Inhibit Protein-Protein Interactions." Biophysical Journal 114, no. 3 (February 2018): 56a—57a. http://dx.doi.org/10.1016/j.bpj.2017.11.362.

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9

Liu, Junyang, Shoubin Tang, Jia-Lei Yan, and Tao Ye. "Design and Synthesis of Novel Helix Mimetics Based on the Covalent H-Bond Replacement and Amide Surrogate." Molecules 28, no. 2 (January 12, 2023): 780. http://dx.doi.org/10.3390/molecules28020780.

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A novel hydrogen bond surrogate-based (HBS) α-helix mimetic was designed by the combination of covalent H-bond replacement and the use of an ether linkage to substitute an amide bond within a short peptide sequence. The new helix template could be placed in position other than the N-terminus of a short peptide, and the CD studies demonstrate that the template adopts stable conformations in aqueous buffer at exceptionally high temperatures.

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10

Wang, Deyun, Min Lu, and Paramjit S Arora. "Inhibition of HIV-1 Fusion by Hydrogen-Bond-Surrogate-Based α Helices." Angewandte Chemie International Edition 47, no. 10 (February 22, 2008): 1879–82. http://dx.doi.org/10.1002/anie.200704227.

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11

Wang, Deyun, Min Lu, and Paramjit S Arora. "Inhibition of HIV-1 Fusion by Hydrogen-Bond-Surrogate-Based α Helices." Angewandte Chemie 120, no. 10 (February 22, 2008): 1905–8. http://dx.doi.org/10.1002/ange.200704227.

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12

Mahon, Andrew B., and Paramjit S. Arora. "Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices." Chem. Commun. 48, no. 10 (2012): 1416–18. http://dx.doi.org/10.1039/c1cc14730g.

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13

Miller, Stephen E., Paul F. Thomson, and Paramjit S. Arora. "Synthesis of Hydrogen‐Bond Surrogate α‐Helices as Inhibitors of Protein‐Protein Interactions." Current Protocols in Chemical Biology 6, no. 2 (June 2014): 101–16. http://dx.doi.org/10.1002/9780470559277.ch130202.

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14

Patgiri, Anupam, Monica Z. Menzenski, Andrew B. Mahon, and Paramjit S. Arora. "Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach." Nature Protocols 5, no. 11 (October 28, 2010): 1857–65. http://dx.doi.org/10.1038/nprot.2010.146.

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15

Chapman, Ross N., Gianluca Dimartino, and Paramjit S. Arora. "A Highly Stable Short α-Helix Constrained by a Main-Chain Hydrogen-Bond Surrogate." Journal of the American Chemical Society 126, no. 39 (October 2004): 12252–53. http://dx.doi.org/10.1021/ja0466659.

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16

Bao, Ju, Xiao Y. Dong, John Z. H. Zhang, and Paramjit S. Arora. "Dynamical Binding of Hydrogen-Bond Surrogate Derived Bak Helices to Antiapoptotic Protein Bcl-xL." Journal of Physical Chemistry B 113, no. 11 (March 19, 2009): 3565–71. http://dx.doi.org/10.1021/jp809810z.

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17

Chu, Jiaxiang, Timothy G. Carroll, Guang Wu, Joshua Telser, Roman Dobrovetsky, and Gabriel Ménard. "Probing Hydrogen Atom Transfer at a Phosphorus(V) Oxide Bond Using a “Bulky Hydrogen Atom” Surrogate: Analogies to PCET." Journal of the American Chemical Society 140, no. 45 (November 2018): 15375–83. http://dx.doi.org/10.1021/jacs.8b09063.

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18

Liu, Jie, Deyun Wang, Qi Zheng, Min Lu, and Paramjit S. Arora. "Atomic Structure of a Short α-Helix Stabilized by a Main Chain Hydrogen-Bond Surrogate." Journal of the American Chemical Society 130, no. 13 (April 2008): 4334–37. http://dx.doi.org/10.1021/ja077704u.

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19

Wang, Deyun, Kang Chen, John L. Kulp, and Paramjit S. Arora. "Evaluation of Biologically Relevant Short α-Helices Stabilized by a Main-Chain Hydrogen-Bond Surrogate." Journal of the American Chemical Society 128, no. 28 (July 2006): 9248–56. http://dx.doi.org/10.1021/ja062710w.

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20

Patgiri, Anupam, Andrea L. Jochim, and Paramjit S. Arora. "A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-Helical Conformation." Accounts of Chemical Research 41, no. 10 (October 21, 2008): 1289–300. http://dx.doi.org/10.1021/ar700264k.

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21

Pal, Sunit, and Erode N. Prabhakaran. "Trimodular Solution‐Phase Protocol for Rapid Large‐Scale Synthesis of Hydrogen Bond Surrogate‐Constrained α‐Helicomimics." European Journal of Organic Chemistry 2021, no. 11 (March 5, 2021): 1714–19. http://dx.doi.org/10.1002/ejoc.202001359.

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22

Henchey, Laura K., Swati Kushal, Ramin Dubey, Ross N. Chapman, Bogdan Z. Olenyuk, and Paramjit S. Arora. "Inhibition of Hypoxia Inducible Factor 1—Transcription Coactivator Interaction by a Hydrogen Bond Surrogate α-Helix." Journal of the American Chemical Society 132, no. 3 (January 27, 2010): 941–43. http://dx.doi.org/10.1021/ja9082864.

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23

Douse, Christopher H., Sabrina J. Maas, Jemima C. Thomas, James A. Garnett, Yunyun Sun, Ernesto Cota, and Edward W. Tate. "Crystal Structures of Stapled and Hydrogen Bond Surrogate Peptides Targeting a Fully Buried Protein–Helix Interaction." ACS Chemical Biology 9, no. 10 (August 6, 2014): 2204–9. http://dx.doi.org/10.1021/cb500271c.

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24

Pal, Sunit, and Erode N. Prabhakaran. "Hydrogen bond surrogate stabilized water soluble 310-helix from a disordered pentapeptide containing coded α-amino acids." Tetrahedron Letters 59, no. 26 (June 2018): 2515–19. http://dx.doi.org/10.1016/j.tetlet.2018.05.029.

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25

Henchey, Laura K., Swati Kushal, Ramin Dubey, Ross N. Chapman, Bogdan Z. Olenyuk, and Paramjit S. Arora. "Correction to Inhibition of Hypoxia Inducible Factor 1–Transcription Coactivator Interaction by a Hydrogen Bond Surrogate α-Helix." Journal of the American Chemical Society 134, no. 18 (April 27, 2012): 8000. http://dx.doi.org/10.1021/ja302676m.

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26

Chapman, Ross N., and Paramjit S. Arora. "Optimized Synthesis of Hydrogen-Bond Surrogate Helices: Surprising Effects of Microwave Heating on the Activity of Grubbs Catalysts." Organic Letters 8, no. 25 (December 2006): 5825–28. http://dx.doi.org/10.1021/ol062443z.

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27

Patgiri, Anupam, Michael R. Witten, and Paramjit S. Arora. "Solid phase synthesis of hydrogen bond surrogate derived α-helices: resolving the case of a difficult amide coupling." Organic & Biomolecular Chemistry 8, no. 8 (2010): 1773. http://dx.doi.org/10.1039/c000905a.

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28

Henchey, Laura K., Jason R. Porter, Indraneel Ghosh, and Paramjit S. Arora. "High Specificity in Protein Recognition by Hydrogen-Bond-Surrogate α-Helices: Selective Inhibition of the p53/MDM2 Complex." ChemBioChem 11, no. 15 (September 6, 2010): 2104–7. http://dx.doi.org/10.1002/cbic.201000378.

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29

Wang, Deyun, Wei Liao, and Paramjit S. Arora. "Enhanced Metabolic Stability and Protein-Binding Properties of Artificial α Helices Derived from a Hydrogen-Bond Surrogate: Application to Bcl-xL." Angewandte Chemie 117, no. 40 (October 14, 2005): 6683–87. http://dx.doi.org/10.1002/ange.200501603.

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30

Wang, Deyun, Wei Liao, and Paramjit S. Arora. "Enhanced Metabolic Stability and Protein-Binding Properties of Artificial α Helices Derived from a Hydrogen-Bond Surrogate: Application to Bcl-xL." Angewandte Chemie International Edition 44, no. 40 (October 14, 2005): 6525–29. http://dx.doi.org/10.1002/anie.200501603.

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31

Gulotta, Maria Rita, Riccardo Brambilla, Ugo Perricone, and Andrea Brancale. "A Rational Design of α-Helix-Shaped Peptides Employing the Hydrogen-Bond Surrogate Approach: A Modulation Strategy for Ras-RasGRF1 Interaction in Neuropsychiatric Disorders." Pharmaceuticals 14, no. 11 (October 28, 2021): 1099. http://dx.doi.org/10.3390/ph14111099.

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In the last two decades, abnormal Ras (rat sarcoma protein)–ERK (extracellular signal-regulated kinase) signalling in the brain has been involved in a variety of neuropsychiatric disorders, including drug addiction, certain forms of intellectual disability, and autism spectrum disorder. Modulation of membrane-receptor-mediated Ras activation has been proposed as a potential target mechanism to attenuate ERK signalling in the brain. Previously, we showed that a cell penetrating peptide, RB3, was able to inhibit downstream signalling by preventing RasGRF1 (Ras guanine nucleotide-releasing factor 1), a neuronal specific GDP/GTP exchange factor, to bind Ras proteins, both in brain slices and in vivo, with an IC50 value in the micromolar range. The aim of this work was to mutate and improve this peptide through computer-aided techniques to increase its inhibitory activity against RasGRF1. The designed peptides were built based on the RB3 peptide structure corresponding to the α-helix of RasGRF1 responsible for Ras binding. For this purpose, the hydrogen-bond surrogate (HBS) approach was exploited to maintain the helical conformation of the designed peptides. Finally, residue scanning, MD simulations, and MM-GBSA calculations were used to identify 18 most promising α-helix-shaped peptides that will be assayed to check their potential activity against Ras-RasGRF1 and prevent downstream molecular events implicated in brain disorders.

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32

Akparov, Valery, Nikolay Sokolenko, Vladimir Timofeev, and Inna Kuranova. "Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine." Acta Crystallographica Section F Structural Biology Communications 71, no. 10 (September 23, 2015): 1335–40. http://dx.doi.org/10.1107/s2053230x15016799.

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Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp 3-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps. The enzyme–inhibitor complex and 329 water molecules were further refined to a crystallographic R factor of 0.159. The differences in conformation between the complexed and uncomplexed forms of carboxypeptidase B are shown. The inhibitor is bound in a curved conformation in the active-site cleft, and the sulfamide group is bound to the Zn ion in an asymmetric bidentate fashion. The complex is stabilized by hydrogen bonds between the N1/N2 guanidine group of the inhibitor and the Asp255 carboxyl of the enzyme. The side-chain CH2 groups of the inhibitor are in van der Waals contact with Leu203 and Ile247 in the enzyme. This study provides useful clues concerning how the transition state of arginine may bind to carboxypeptidase B and therefore provides an insight into the structural basis of carboxypeptidase B selectivity, which is useful for the rational design of a carboxypeptidase with improved selectivity for industrial recombinant pro-insulin processing.

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33

Malquin, N., K. Rahgoshay, N. Lensen, G. Chaume, E. Miclet, and T. Brigaud. "CF2H as a hydrogen bond donor group for the fine tuning of peptide bond geometry with difluoromethylated pseudoprolines." Chemical Communications 55, no. 83 (2019): 12487–90. http://dx.doi.org/10.1039/c9cc05771d.

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CF₂H-Pseudoprolines obtained from difluoroacetaldehyde hemiacetal and serine are stable proline surrogates. An intramolecular H-bond due to the CF₂H group is promoting an exceptionally high content of cis-amide bond conformation.

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34

Kawabata, Takeo, Changsheng Jiang, Kazuhiro Hayashi, Kazunori Tsubaki, Tomoyuki Yoshimura, Swapan Majumdar, Takahiro Sasamori, and Norihiro Tokitoh. "Axially Chiral Binaphthyl Surrogates with an Inner N−H−N Hydrogen Bond." Journal of the American Chemical Society 131, no. 1 (January 14, 2009): 54–55. http://dx.doi.org/10.1021/ja808213r.

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35

Weidkamp, Andreas J., and Martin Oestreich. "Metal-free transfer hydrochlorination of internal C–C triple bonds with a bicyclo[3.1.0]hexane-based surrogate releasing two molecules of hydrogen chloride." Chemical Communications 58, no. 7 (2022): 973–76. http://dx.doi.org/10.1039/d1cc06591b.

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A non-protic surrogate that contains two molecules of HCl for the synthesis of alkenyl chlorides from internal alkynes is reported. The HCl transfer is catalyzed by B(C6F5)3 and driven by release of strain and aromatization.

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36

Mhatre, Chinmay V., Jacob J. Wardzala, Priyanka B. Shukla, Mayank Agrawal, and J. Karl Johnson. "Calculation of Self, Corrected, and Transport Diffusivities of Isopropyl Alcohol in UiO-66." Nanomaterials 13, no. 11 (June 2, 2023): 1793. http://dx.doi.org/10.3390/nano13111793.

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The UiO-6x family of metal-organic frameworks has been extensively studied for applications in chemical warfare agent (CWA) capture and destruction. An understanding of intrinsic transport phenomena, such as diffusion, is key to understanding experimental results and designing effective materials for CWA capture. However, the relatively large size of CWAs and their simulants makes diffusion in the small-pored pristine UiO-66 very slow and hence impractical to study directly with direct molecular simulations because of the time scales required. We used isopropanol (IPA) as a surrogate for CWAs to investigate the fundamental diffusion mechanisms of a polar molecule within pristine UiO-66. IPA can form hydrogen bonds with the μ3-OH groups bound to the metal oxide clusters in UiO-66, similar to some CWAs, and can be studied by direct molecular dynamics simulations. We report self, corrected, and transport diffusivities of IPA in pristine UiO-66 as a function of loading. Our calculations highlight the importance of the accurate modeling of the hydrogen bonding interactions on diffusivities, with about an order of magnitude decrease in diffusion coefficients when the hydrogen bonding between IPA and the μ3-OH groups is included. We found that a fraction of the IPA molecules have very low mobility during the course of a simulation, while a small fraction are highly mobile, exhibiting mean square displacements far greater than the ensemble average.

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37

Kaur, Richie, Brandi M. Hudson, Joseph Draper, Dean J. Tantillo, and Cort Anastasio. "Aqueous reactions of organic triplet excited states with atmospheric alkenes." Atmospheric Chemistry and Physics 19, no. 7 (April 12, 2019): 5021–32. http://dx.doi.org/10.5194/acp-19-5021-2019.

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Abstract. Triplet excited states of organic matter are formed when colored organic matter (i.e., brown carbon) absorbs light. While these “triplets” can be important photooxidants in atmospheric drops and particles (e.g., they rapidly oxidize phenols), very little is known about their reactivity toward many classes of organic compounds in the atmosphere. Here we measure the bimolecular rate constants of the triplet excited state of benzophenone (3BP∗), a model species, with 17 water-soluble C3–C6 alkenes that have either been found in the atmosphere or are reasonable surrogates for identified species. Measured rate constants (kALK+3BP∗) vary by a factor of 30 and are in the range of (0.24–7.5) ×109 M−1 s−1. Biogenic alkenes found in the atmosphere – e.g., cis-3-hexen-1-ol, cis-3-hexenyl acetate, and methyl jasmonate – react rapidly, with rate constants above 1×109 M−1 s−1. Rate constants depend on alkene characteristics such as the location of the double bond, stereochemistry, and alkyl substitution on the double bond. There is a reasonable correlation between kALK+3BP∗ and the calculated one-electron oxidation potential (OP) of the alkenes (R2=0.58); in contrast, rate constants are not correlated with bond dissociation enthalpies, bond dissociation free energies, or computed energy barriers for hydrogen abstraction. Using the OP relationship, we estimate aqueous rate constants for a number of unsaturated isoprene and limonene oxidation products with 3BP∗: values are in the range of (0.080–1.7) ×109 M−1 s−1, with generally faster values for limonene products. Rate constants with less reactive triplets, which are probably more environmentally relevant, are likely roughly 25 times slower. Using our predicted rate constants, along with values for other reactions from the literature, we conclude that triplets are probably minor oxidants for isoprene- and limonene-related compounds in cloudy or foggy atmospheres, except in cases in which the triplets are very reactive.

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38

Guan, X. H., D. L. Li, C. Shang, and G. H. Chen. "Role of carboxylic and phenolic groups in NOM adsorption on minerals: a review." Water Supply 6, no. 6 (December 1, 2006): 155–64. http://dx.doi.org/10.2166/ws.2006.959.

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This paper presented the current state of our understanding of the roles of carboxylic and phenolic groups in NOM adsorption and reviewed the contradictory opinions in the literatures. Previous studies carried out by other researchers indicated that aromatic carboxylates were adsorbed onto metal (hydr)oxides via outer-sphere complexes under most conditions and phenolic groups were very crucial for formation of inner-sphere complexes between organic acids and metal (hydr)oxides. Adsorption test with in-situ ATR-FTIR spectroscopic investigation were carried out to verify the role of aromatic carboxylic and phenolic groups in the NOM adsorption onto aluminium hydroxide surfaces by using a series of aromatic carboxylic acids and dihydroxybenzoic acids as the surrogate of NOM. Our studies suggested that the formation of outer-sphere complexes dominated the adsorption of most of the aromatic carboxylates over the pH range of 5–9; inner-sphere complexes were only detected at some pH levels for some aromatic carboxylates adsorption; and the aromatic carboxylates were most likely to be adsorbed to the first surface layer of hydroxyl groups and water molecules without forming coordinative bonds with the aluminium hydroxide surfaces but strong hydrogen bonds were formed in this process. Our study also revealed that (1) the presence of phenolic groups can increase the interaction strength of carboxylate groups with aluminium hydroxide; (2) chelate formation involving a carboxylate oxygen atom and ortho-phenolic-oxygen is important for the adsorption of organic matter on aluminium hydroxide at acidic pH; and 3) the phenolic groups adjacent to each other are more important than the carboxylic groups at alkaline pH for organic matter adsorption.

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39

Roy, Siddhartha, Piya Ghosh, Israr Ahmed, Madhumita Chakraborty, Gitashri Naiya, and Basusree Ghosh. "Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions." Biomedicines 6, no. 4 (December 18, 2018): 118. http://dx.doi.org/10.3390/biomedicines6040118.

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Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as “undruggable”. Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these macromolecular interactions is an α-helix, raising possibilities that an appropriate conformationally-constrained α-helical peptide may specifically disrupt these interactions. Several methods for conformationally constraining peptides to the α-helical conformation have been developed, including stapling, covalent surrogates of hydrogen bonds and incorporation of unnatural amino acids that restrict the conformational space of the peptide. We will discuss these methods and several case studies where constrained α-helices have been used as building blocks for appropriate molecules. Unlike small molecules, the delivery of these short peptides to their targets is not straightforward as they may possess unfavorable cell penetration and ADME properties. Several methods have been developed in recent times to overcome some of these problems. We will discuss these issues and the prospects of this class of molecules as drugs.

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40

Hummel, Darius, Andreas Fath, Thilo Hofmann, and Thorsten Hüffer. "Additives and polymer composition influence the interaction of microplastics with xenobiotics." Environmental Chemistry 18, no. 3 (2021): 101. http://dx.doi.org/10.1071/en21030.

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Environmental contextThe effects of the presence of polymer additives and polymeric structure on sorption of xenobiotics to microplastics remain unclear. Our results combined data from experimental sorption batch experiments using three environmentally relevant model sorbates with confocal microscopy. This provides clear evidence that both factors play a major role in sorption strength and the underlying sorption process, affecting sorption onto the particle surface and partitioning into the bulk polymer. AbstractMicroplastics are particulate contaminants of global concern. Interactions of microplastics with organic contaminants are frequently studied with commercially available polymer materials as surrogates. The influence of the polymer structure (i.e. internal 3D polymer geometry and monomer chain length) and the presence of additives on their interactions with xenobiotics remains unclear. This work investigates sorption of three sorbates of environmental concern to two polyamide (PA) and two polyvinyl chloride (PVC) sorbents of different molecular composition and additive content, respectively. Sorption was studied using complementary data from sorption isotherms and confocal laser-scanning microscopy. The additives in PVC increased sorption affinity owing to an increased sorbent hydrophobicity and a higher void volume within the polymer. Surface area normalisation indicated surface adsorption for unplasticised PVC and absorption for 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH)-plasticised PVC, which were confirmed using confocal laser-scanning microscopy. The strong sorption to PA was mainly driven by hydrogen-bond interactions. The contribution depended on the molecular features of the sorbent and the sorbate. Confocal laser-scanning microscopy showed that PA6 was taking up more sorbate into its bulk polymer matrix than PA12, the two being different in their chemical composition. This difference could be attributed to the higher swelling capability of PA6. The results emphasise that the molecular structure of the polymer and the presence of additives have to be taken into consideration when sorption of organic substances to plastics is investigated.

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41

Dragone, Martina, Rinaldo Grazioso, Gianluca D’Abrosca, Ilaria Baglivo, Rosa Iacovino, Sabrina Esposito, Antonella Paladino, et al. "Copper (I) or (II) Replacement of the Structural Zinc Ion in the Prokaryotic Zinc Finger Ros Does Not Result in a Functional Domain." International Journal of Molecular Sciences 23, no. 19 (September 20, 2022): 11010. http://dx.doi.org/10.3390/ijms231911010.

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A strict interplay is known to involve copper and zinc in many cellular processes. For this reason, the results of copper’s interaction with zinc binding proteins are of great interest. For instance, copper interferences with the DNA-binding activity of zinc finger proteins are associated with the development of a variety of diseases. The biological impact of copper depends on the chemical properties of its two common oxidation states (Cu(I) and Cu(II)). In this framework, following the attention addressed to unveil the effect of metal ion replacement in zinc fingers and in zinc-containing proteins, we explore the effects of the Zn(II) to Cu(I) or Cu(II) replacement in the prokaryotic zinc finger domain. The prokaryotic zinc finger protein Ros, involved in the horizontal transfer of genes from A. tumefaciens to a host plant infected by it, belongs to a family of proteins, namely Ros/MucR, whose members have been recognized in different bacteria symbionts and pathogens of mammals and plants. Interestingly, the amino acids of the coordination sphere are poorly conserved in most of these proteins, although their sequence identity can be very high. In fact, some members of this family of proteins do not bind zinc or any other metal, but assume a 3D structure similar to that of Ros with the residues replacing the zinc ligands, forming a network of hydrogen bonds and hydrophobic interactions that surrogates the Zn-coordinating role. These peculiar features of the Ros ZF domain prompted us to study the metal ion replacement with ions that have different electronic configuration and ionic radius. The protein was intensely studied as a perfectly suited model of a metal-binding protein to study the effects of the metal ion replacement; it appeared to tolerate the Zn to Cd substitution, but not the replacement of the wildtype metal by Ni(II), Pb(II) and Hg(II). The structural characterization reported here gives a high-resolution description of the interaction of copper with Ros, demonstrating that copper, in both oxidation states, binds the protein, but the replacement does not give rise to a functional domain.

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42

Pal, Sunit. "Impact of Hydrogen‐Bond Surrogate Model on Helix Stabilization and Development of Protein‐Protein Interaction Inhibitors." ChemistrySelect 8, no. 10 (March 9, 2023). http://dx.doi.org/10.1002/slct.202204207.

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43

Patgiri, Anupam, Andrea L. Jochim, and Paramjit S. Arora. "ChemInform Abstract: A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-Helical Conformation." ChemInform 40, no. 3 (January 20, 2009). http://dx.doi.org/10.1002/chin.200903252.

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44

Nazzaro, Alex, Brandon Lu, Nicholas Sawyer, Andrew M. Watkins, and Paramjit S. Arora. "Macrocyclic β‐Sheets Stabilized by Hydrogen Bond Surrogates." Angewandte Chemie, May 11, 2023. http://dx.doi.org/10.1002/ange.202303943.

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45

Nazzaro, Alex, Brandon Lu, Nicholas Sawyer, Andrew M. Watkins, and Paramjit S. Arora. "Macrocyclic β‐Sheets Stabilized by Hydrogen Bond Surrogates." Angewandte Chemie International Edition, May 11, 2023. http://dx.doi.org/10.1002/anie.202303943.

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