51
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Huynh TP, Pietrzyk-Le A, Bikram K C C, Noworyta KR, Sobczak JW, Sharma PS, D'Souza F, Kutner W. Electrochemically synthesized molecularly imprinted polymer of thiophene derivatives for flow-injection analysis determination of adenosine-5'-triphosphate (ATP). Biosens Bioelectron 2012; 41:634-41. [PMID: 23131778 DOI: 10.1016/j.bios.2012.09.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/16/2012] [Accepted: 09/21/2012] [Indexed: 12/18/2022]
Abstract
Two selective chemosensors for adenosine-5'-triphosphate (ATP) determination featuring molecularly imprinted polymer (MIP) film recognition units were fabricated. For imprinting, three different thiophene derivatives were used as functional monomers. That is, the uracil substituent of bis(2,2'-bithienyl)methane 2 complementarily H-bond paired the adenine moiety of ATP, the boronic acid substituent of thiophene 3 covalently bound vicinal diols of the ribofuranose moiety, and amide substituents of bis(2,2'-bithienyl)methanes 4 bound to the pyrophosphate moieties. Different binding motifs adopted for the ATP recognition and the structure of the supramolecular pre-polymerization complex were optimized with the DFT computing at the B3LYP/3-21G((*)) level. MIP films were prepared by potentiodynamic electropolymerization of this complex with the imprinting factor of 9.47±0.2. An analytical signal was transduced with a 10-MHz resonator of EQCM and a Pt electrode for the piezoelectric microgravimetry (PM) and capacitive impedometry (CI) determination of ATP, respectively, under FIA conditions. Analytical properties of the MIP film were unraveled by spectroscopic ellipsometry, XPS, IRRAS, and DPV. The limit of detection was 0.1 and 0.2 μM for the PM and CI chemosensor, respectively, being an order of magnitude lower than the ATP concentration in biological systems. Moreover, cross-selectivity was demonstrated with the adenosine-5'-diphosphate (ADP) imprinting and ATP discrimination.
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Affiliation(s)
- Tan-Phat Huynh
- Institute of Physical Chemistry (IPC PAS), Kasprzaka 44/52, 01-224 Warsaw, Poland
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52
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Ma C, Chen H, Han R, He H, Zeng W. Fluorescence detection of adenosine triphosphate using smart probe. Anal Biochem 2012; 429:8-10. [PMID: 22759778 DOI: 10.1016/j.ab.2012.06.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/19/2012] [Accepted: 06/24/2012] [Indexed: 12/16/2022]
Abstract
A novel fluorescent probe for adenosine triphosphate (ATP) assay based on DNA ligation is proposed in this article. This approach uses a novel smart probe, T4 DNA ligase, and two short oligonucleotides. In the presence of ATP, the T4 DNA ligase catalyzes the ligation reaction and the ligation product restores the fluorescence of the smart probe. This method is very sensitive with a 0.5-nM limit of detection. Compared with current assay methods, the strategy is simpler, cheaper, and 40 times more sensitive.
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Affiliation(s)
- Changbei Ma
- School of Biological Science and Technology, Central South University, Changsha 410013, China.
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53
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Yan L, Ye Z, Peng C, Zhang S. A new perylene diimide-based fluorescent chemosensor for selective detection of ATP in aqueous solution. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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54
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Raghunathan D, Gayen S, Kumar A, Hunke C, Grüber G, Verma CS. Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Gö1. J Bioenerg Biomembr 2012; 44:213-24. [PMID: 22350011 DOI: 10.1007/s10863-012-9410-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/08/2012] [Indexed: 10/28/2022]
Abstract
The interaction of the nucleotide-binding subunit B with subunit F is essential in coupling of ion pumping and ATP synthesis in A(1)A(O) ATP synthases. Here we provide structural and thermodynamic insights on the nucleotide binding to the surface of subunits B and F of Methanosarcina mazei Gö1 A(1)A(O) ATP synthase, which initiated migration to its final binding pocket via two transitional intermediates on the surface of subunit B. NMR- and fluorescence spectroscopy as well as ITC data combined with molecular dynamics simulations of the nucleotide bound subunit B and nucleotide bound B-F complex in explicit solvent, suggests that subunit F is critical for the migration to and eventual occupancy of the final binding site by the nucleotide of subunit B. Rotation of the C-terminus and conformational changes in subunit B are initiated upon binding with subunit F causing a perturbation that leads to the migration of ATP from the transition site 1 through an intermediate transition site 2 to the final binding site 3. This mechanism is elucidated on the basis of change in binding affinity for the nucleotide at the specific sites on subunit B upon complexation with subunit F. The change in enthalpy is further explained based on the fluctuating local environment around the binding sites.
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55
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Rostami A, Taylor MS. Polymers for Anion Recognition and Sensing. Macromol Rapid Commun 2011; 33:21-34. [DOI: 10.1002/marc.201100528] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/12/2011] [Indexed: 01/25/2023]
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56
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011; 50:12201-4. [DOI: 10.1002/anie.201106177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Indexed: 01/23/2023]
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57
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Wilger DJ, Park JH, Hughes RM, Cuellar ME, Waters ML. Induced-Fit Binding of a Polyproline Helix by a β-Hairpin Peptide. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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58
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Liu J, Morikawa MA, Kimizuka N. Conversion of molecular information by luminescent nanointerface self-assembled from amphiphilic Tb(III) complexes. J Am Chem Soc 2011; 133:17370-4. [PMID: 21932810 DOI: 10.1021/ja2057924] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A novel amphiphilic Tb(3+) complex (TbL(+)) having anionic bis(pyridine) arms and a hydrophobic alkyl chain is developed. It spontaneously self-assembles in water and gives stable vesicles that show sensitized luminescence of Tb(3+) ions at neutral pH. This TbL(+) complex is designed to show coordinative unsaturation, i.e., water molecules occupy some of the first coordination spheres and are replaceable upon binding of phosphate ions. These features render TbL(+) self-assembling receptor molecules which show increase in the luminescence intensity upon binding of nucleotides. Upon addition of adenosine triphosphate (ATP), significant amplification of luminescent intensity was observed. On the other hand, ADP showed moderately increased luminescence and almost no enhancement was observed for AMP. Very interestingly, the increase in luminescence intensity observed for ATP and ADP showed sigmoidal dependence on the concentration of added nucleotides. It indicates positive cooperative binding of these nucleotides to TbL(+) complexes preorganized on the vesicle surface. Self-assembly of amphiphilic Tb(3+) receptor complexes provides nanointerfaces which selectively convert and amplify molecular information of high energy phosphates linked by phosphoanhydride bonds into luminescence intensity changes.
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Affiliation(s)
- Jing Liu
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
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59
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He Y, Wang ZG, Tang HW, Pang DW. Low background signal platform for the detection of ATP: when a molecular aptamer beacon meets graphene oxide. Biosens Bioelectron 2011; 29:76-81. [PMID: 21889887 DOI: 10.1016/j.bios.2011.07.069] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/23/2011] [Accepted: 07/27/2011] [Indexed: 11/28/2022]
Abstract
A novel molecular aptamer beacon (MAB) was designed by integrating a single-labeled hairpin-shaped aptamer and graphene oxide (GO). The hairpin-shaped aptamer was constructed with anti-ATP aptamer and another five nucleotides added to the 5'-end of the aptamer which are complementary to nucleotides at the 3'-end of the aptamer to form a hairpin-shaped probe. This newly designed MAB which acts as a low background signal platform was used for the ATP detection based on long-range resonance energy transfer (LrRET). In the absence of ATP, the adsorption of the dye-labeled hairpin-shaped aptamer on GO makes the dyes close proximity to GO surface resulting in high efficiency quenching of fluorescence of the dyes. Therefore, the fluorescence of the designed MAB is completely quenched by GO, and the system shows very low background. Conversely, and very importantly, upon the adding of ATP, the quenched fluorescence is recovered significantly, and ATP can be detected in a wide range of 5-2500μM with a detection limit of 2μM and good selectivity. Moreover, when the GO-based MAB was used in cellular ATP assays, preeminent fluorescence signals were obtained, thus the platform of GO-based MAB could be used to detect ATP in real-world samples.
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Affiliation(s)
- Yue He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Research Center for Nanobiology and Nanomedicine (MOE 985 Innovative Platform), Wuhan Institute of Biotechnology, Wuhan University, Wuhan, 430072, PR China
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60
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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61
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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62
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Xu Z, Spring DR, Yoon J. Fluorescent sensing and discrimination of ATP and ADP based on a unique sandwich assembly of pyrene-adenine-pyrene. Chem Asian J 2011; 6:2114-22. [PMID: 21506284 DOI: 10.1002/asia.201100120] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Indexed: 11/07/2022]
Abstract
It is still a challenging task to discriminate adenosine-5'-triphosphate (ATP) from various nucleoside triphosphates, such as GTP, CTP, UTP, and TTP. The ability to distinguish ATP from adenosine diphosphate (ADP) by fluorescent signals is also urgently desired. Herein, we report two pyrene-based zinc complexes as nucleoside polyphosphate receptors with high selectivity for ATP and ADP based on fluorescence and NMR studies. A unique pyrene-adenine-pyrene sandwich assembly was observed in the case of compound 1 with ATP or ADP, resulting in the increase of monomer fluorescence intensity; whereas the other bases of nucleoside triphosphates, such as GTP, CTP, UTP, and TTP were not sandwiched, resulting in a switch in the monomer-excimer fluorescence of pyrene. The different binding patterns of various nucleobases with a pyrene-pyrene assembly make 1 a highly selective fluorescent sensor for ANP (N=di, tri). In the case of compound 2, the first 0.5 equivalents of ATP induced a strong excimer emission, whilst ADP induced a large enhancement in the monomeric fluorescent peak. This fluorescence change makes 2 an efficient sensor to discriminate ATP from ADP.
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Affiliation(s)
- Zhaochao Xu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Korea
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63
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Kuchelmeister HY, Schmuck C. Nucleotide recognition in water by a guanidinium-based artificial tweezer receptor. Chemistry 2011; 17:5311-8. [PMID: 21462273 DOI: 10.1002/chem.201003393] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Indexed: 11/06/2022]
Abstract
The water-soluble tweezer receptor 1 with two symmetric peptidic arms, which are connected by an aromatic scaffold and contain lysine, phenylalanine, and a guanidinium-based anion-binding site as headgroup, has been synthesized. UV/Vis-derived Job plots show that the receptor forms 1:1 complexes with nucleotides and phosphate in buffered water at neutral pH. Binding constants have been determined by fluorescence and UV/Vis spectroscopy. All nucleotides tested were bound very efficiently, even in pure water, with binding constants between 10(4) and 10(5) M(-1) . Interestingly, all mononucleotides were bound much stronger than phosphate by a factor of at least 5 to 10. Furthermore 1 favors the binding of adenosine monophosphate (AMP) over adenosine diphosphate (ADP) and adenosine triphosphate (ATP), which is unprecedented for artificial nucleotide receptors reported so far. According to NMR spectroscopy and molecular modeling studies, the efficient binding is a result of strong electrostatic contacts supported by π-π interactions with the nucleobase within the cavity-shaped receptor.
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Affiliation(s)
- Hannes Y Kuchelmeister
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
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64
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Santiveri CM, Jiménez MA. Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides. Biopolymers 2011; 94:779-90. [PMID: 20564027 DOI: 10.1002/bip.21436] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid 28006, Spain
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65
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Stewart AL, Park JH, Waters ML. Redesign of a WW domain peptide for selective recognition of single-stranded DNA. Biochemistry 2011; 50:2575-84. [PMID: 21332166 DOI: 10.1021/bi101116a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A β-sheet miniprotein based on the FBP11 WW1 domain sequence has been redesigned for the molecular recognition of ssDNA. A previous report showed that a β-hairpin peptide dimer, (WKWK)(2), binds ssDNA with low micromolar affinity but with little selectivity over duplex DNA. This report extends those studies to a three-stranded β-sheet miniprotein designed to mimic the OB-fold. The new peptide binds ssDNA with low micromolar affinity and shows about 10-fold selectivity for ssDNA over duplex DNA. The redesigned peptide no longer binds its native ligand, the polyproline helix, confirming that the peptide has been redesigned for the function of binding ssDNA. Structural studies provide evidence that this peptide consists of a well-structured β-hairpin made of strands 2 and 3 with a less structured first strand that provides affinity for ssDNA but does not improve the stability of the full peptide. These studies provide insight into protein-DNA interactions as well as a novel example of protein redesign.
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Affiliation(s)
- Amanda L Stewart
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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66
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Xu Y, Malkovskiy A, Wang Q, Pang Y. Molecular assembly of a squaraine dye with cationic surfactant and nucleotides: its impact on aggregation and fluorescence response. Org Biomol Chem 2011; 9:2878-84. [PMID: 21373660 DOI: 10.1039/c0ob01061h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescent system has been assembled by using ATP, surfactant, and a squaraine dye in an aqueous buffer solution. In the system, a cationic surfactant such as cetyl trimethyl ammonium bromide (CTAB) forms a sphere-like micelle, whose positive charge at the surface of the micelle attracts the negatively charged ATP to form a unique organized nanostructure. Such an organized system is shown to interact with the squaraine dye (SQ) to perturb its aggregate structure, thereby generating the optical response. The nanostructure of the assembly has been characterized by dynamic light-scattering (DLS) and atomic force microscopy (AFM). The unique feature of the developed sensing system is that the analytes ATP form part of the assembly structure. The system utilizes forces such as electrostatic interaction and π-π stacking of the aromatic segment of ATP and SQ to achieve the selective detection of ATP.
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Affiliation(s)
- Yongqian Xu
- Department of Chemistry & Maurice Morton Institute of Polymer Science, The University of Akron, Akron, OH 44325, USA
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67
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Ryu N, Hachisako H. Functionalization of methyl orange using cationic peptide amphiphile: colorimetric discrimination between ATP and ADP at pH 2.0. Org Biomol Chem 2011; 9:2000-6. [PMID: 21283871 DOI: 10.1039/c0ob00437e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A solvatochromic and non-fluorescent acid-base indicator, methyl orange (MO) was applied to colorimetric discrimination between adenosine triphosphate (ATP) and the corresponding diphosphate (ADP) at pH 2.0 in the presence of L-glutamic acid-derived cationic peptide amphiphile 1. This method is based on the fact that the amphiphile 1 can prevent MO from protonation even at pH 2.0. No similar colour change was observed when ADP was added instead of ATP under the same conditions. The effect of the molecular structure of several peptide amphiphiles and dyes was also investigated.
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Affiliation(s)
- Naoya Ryu
- Division of Applied Chemistry, Graduate School of Engineering, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
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68
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Patel K, Goyal B, Kumar A, Kishore N, Durani S. Cured of “Stickiness”, Poly-l β-Hairpin is Promoted with ll-to-dd Mutation as a Protein and a Hydrolase Mimic. J Phys Chem B 2010; 114:16887-93. [DOI: 10.1021/jp1062572] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kirti Patel
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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69
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Maestro B, Santiveri CM, Jiménez MA, Sanz JM. Structural autonomy of a β-hairpin peptide derived from the pneumococcal choline-binding protein LytA. Protein Eng Des Sel 2010; 24:113-22. [DOI: 10.1093/protein/gzq087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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70
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Cline LL, Waters ML. The structure of well-folded beta-hairpin peptides promotes resistance to peptidase degradation. Biopolymers 2010; 92:502-7. [PMID: 19521977 DOI: 10.1002/bip.21266] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
To investigate the effect of peptide secondary structure on proteolytic resistance, we have synthesized a series of peptides based on a well-folded beta-hairpin, WKWK. Mutations were made within the peptide which either decreased or increased the propensity to form beta-hairpin structures and one scrambled sequence was used as an unstructured control. The peptides were incubated with three different enzymes, alpha-chymotrypsin, trypsin, and pronase E, which represented both specific and non-specific proteases. The reactions were quenched at varying time points and analyzed with RP-HPLC to determine the rate of degradation for each of the peptides. We found that an increase in structure correlates well with an increase in resistance to degradation. We have shown that having both strong side chain interactions and a rigid D-Pro-Gly beta-turn resulted in the most proteolytic resistant peptides. The results from this study suggest that beta-hairpin structure is a viable way to provide added protease resistance to a peptide.
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Affiliation(s)
- Lauren L Cline
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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71
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Klärner FG, Schrader T, Bastkowski F, Polkowska J. Non Covalent Inclusion of Nucleosides and Nucleotides in Water-Soluble Molecular Clips. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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72
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Egel R. Peptide-dominated membranes preceding the genetic takeover by RNA: latest thinking on a classic controversy. Bioessays 2009; 31:1100-9. [PMID: 19708018 DOI: 10.1002/bies.200800226] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It is commonly presumed that abiotic membranes were colonized by proteins later on. Yet, hydrophobic peptides could have formed primordial protein-dominated membranes on their own. In a metabolism-first context, "autocatalytically closed" sets of statistical peptides could organize a self-maintaining protometabolism, assisted by an unfolding set of ribotide-related cofactors. Pairwise complementary ribotide cofactors may have formed docking guides for stochastic peptide formation, before replicating RNA emerged from this subset. Tidally recurring wet-drying cycles and an early onset of photosynthetic activities are considered most likely to meet the thermodynamic requirements. Conceivably, the earliest peptide-dominated vesicles were engaged in light harvesting, together with isoprenoid-tethered pigments, rather than providing an external boundary. Early on, the bulk of prebiotic organic matter can have formed a contiguous layer covering the mineral sediment, held in place by colloidal coherence of a hydrogel matrix. This unconventional scenario assumes a late onset of cellular individualization - perhaps from within, resembling endosporogenesis.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Copenhagen, Denmark.
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73
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Sánchez-García D, Kauffmann B, Kawanami T, Ihara H, Takafuji M, Delville MH, Huc I. Nanosized hybrid oligoamide foldamers: aromatic templates for the folding of multiple aliphatic units. J Am Chem Soc 2009; 131:8642-8. [PMID: 19530733 DOI: 10.1021/ja9019758] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligoamide sequences comprised of both 8-amino-2-quinolinecarboxylic acid "Q" and 6-aminomethyl-2-pyridinecarboxylic acid "P" have been synthesized. It was found that the aliphatic amine of P greatly facilitates amide couplings, as opposed to the aromatic amine of Q, which enabled us to prepare sequences having up to 40 units. The conformation and conformational stability of these oligomers were characterized in the solid state using X-ray crystallography and in solution using NMR and various chromatographic techniques. Q(n) oligomers adopt very stable helically folded conformations whereas P(n) oligomers do not fold and impart conformational preferences distinct from those of Q units. When a P(n) segments is attached at the end of a Q(4) segment, a couple P units appear to follow the folding pattern imposed by the Q(n) segment, but P units remote from the Q(n) segment do not fold. When a P(n) segment is inserted between two Q(4) segments, the P(n) segment adopts the canonical helical conformation imposed by the Q units at least up to two full helical turns (n = 5). However, the overall stability of the helix tends to decrease as the number of P units increases. When noncontiguous P units separated by Q(4) segments are incorporated in a sequence, they all adopt the helical conformation imposed by Q monomers and the overall helix stability increases when helix length increases. For example, a 40mer with a sequence (PQ(4))(8) folds into a rod-like helix spanning over 16 turns with a length of 5.6 nm. This investigation thus demonstrates that remarkably long (nanometers) yet well-defined foldamers can be efficiently synthesized stepwise and that their helical stability may be continuously tuned upon controlling the ratio and sequence of P and Q monomers.
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Affiliation(s)
- David Sánchez-García
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR5248, 2 rue Robert Escarpit, 33607 Pessac, France
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74
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Wu H, He C, Lin Z, Liu Y, Duan C. Metallohelical triangles for selective detection of adenosine triphosphate in aqueous media. Inorg Chem 2009; 48:408-10. [PMID: 19072294 DOI: 10.1021/ic801350h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallohelical triangles consisting of chromophore units and hydrogen-bonding trigger sites were prepared by modulating two tridentate N(2)O units containing amide groups within a central benzene ring at the meta sites, for the selective detection of adenosine trisphosphate in aqueous media over other ribonucleotides.
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Affiliation(s)
- Hongmei Wu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China
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75
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Sawada T, Yoshizawa M, Sato S, Fujita M. Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts. Nat Chem 2009; 1:53-6. [PMID: 21378801 DOI: 10.1038/nchem.100] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 12/04/2008] [Indexed: 11/09/2022]
Abstract
Short nucleotide fragments such as mono- and dinucleotides are generally unable to form stable hydrogen-bonded base pairs or duplexes in water. Within the hydrophobic pockets of enzymes, however, even short fragments form stable duplexes to transmit genetic information. Here, we demonstrate the efficient formation of hydrogen-bonded base pairs from mononucleotides in water through enclathration in the hydrophobic cavities of self-assembled cages. Crystallographic studies and 1H- and 15N-NMR spectroscopy clearly reveals pair-selective recognition of mononucleotides and the selective formation of an anti-Hoogsteen-type base pair in the cage's cavity. Within an analogous expanded cage, dinucleotides are also found to form a stable duplex in water. These results emphasize how hydrogen-bonded base pairing is amplified in a local hydrophobic area isolated from aqueous solution.
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Affiliation(s)
- Tomohisa Sawada
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Japan
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76
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Stewart AL, Waters ML. Structural Effects on ss- and dsDNA Recognition by a β-Hairpin Peptide. Chembiochem 2009; 10:539-44. [DOI: 10.1002/cbic.200800524] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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77
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Matsui J, Nagano J, Miyoshi D, Tamaki K, Sugimoto N. An approach to peptide-based ATP receptors by a combination of random selection, rational design, and molecular imprinting. Biosens Bioelectron 2009; 25:563-7. [PMID: 19497730 DOI: 10.1016/j.bios.2009.01.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 12/27/2008] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
Abstract
Random selection, rational design and molecular imprinting were cooperatively utilized to develop peptide-based ATP synthetic receptors. In this fusion strategy, combinatorial chemistry was utilized for screening a precursor peptide useful for construction of ATP receptors, and rational design was employed in modification of the selected precursor peptide for higher affinity and selectivity. Finally, molecular imprinting was used for pre-organizing the conformation of the precursor peptide as complementary to a target molecule ATP. The fusion strategy appeared to have advantage to sole use of the individual strategy: (1) a low hit-rate of combinatorial chemistry will be improved by customizing a higher order structure of a selected peptide by molecular imprinting, (2) combinatorial chemistry allows us to semi-automatically select components of water-compatible synthetic receptors, (3) rational design improves the selected peptide sequence for better molecularly imprinted receptors. A peptide consisting of a randomly selected sequence and a rationally designed sequence (Resin-Lys-Gly-Arg-Gly-Lys-Gly-Gly-Gly-Glu-Lys-Tyr-Leu-Lys-NHAc) was designed and synthesized as a precursor peptide. The rational design was made according to the sequence of the adenine binding site of biotin carboxylase. The on-beads peptide was cross-linked with dimethyl adipimidate in the presence of ATP. In the saturation binding tests, the cross-linked on-beads peptide showed 5.3 times higher affinity compared to the non-cross-linked peptide with the same sequence. Furthermore, the cross-linked peptide showed improved selectivity; the ratios of binding constants, K((ATP))/K((ADP)) and K((ATP))/K((GTP)), were increased from 2.4 to 19, and from 0.8 to 10, respectively. It would be notable that the peptide without the rationally designed sequence showed no discrimination between ATP and GTP (K((ATP))/K((GTP)) as 0.9), suggesting that the rationally designed site was successfully engaged for recognition of the adenine base.
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Affiliation(s)
- Jun Matsui
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
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78
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79
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Affiliation(s)
- Stefan Kubik
- Fachbereich Chemie-Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Strasse, D-67663, Kaiserslautern, Germany.
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80
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Cline LL, Waters ML. Design of a β-hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA. Org Biomol Chem 2009; 7:4622-30. [DOI: 10.1039/b913024a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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81
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Ghosh A, Shrivastav A, Jose DA, Mishra SK, Chandrakanth CK, Mishra S, Das A. Colorimetric sensor for triphosphates and their application as a viable staining agent for prokaryotes and eukaryotes. Anal Chem 2008; 80:5312-9. [PMID: 18543950 DOI: 10.1021/ac8005022] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The chromogenic complex 1 x Zn (where 1 is (E)-4-(4-dimethylamino-phenylazo)-N,N-bispyridin-2-ylmethyl-benzenesulfonamide) showed high affinity toward the phosphate ion in tetrabutylammonium phosphate in acetonitrile solution and could preferentially bind to adenosine triphosphate (ATP) in aqueous solution at physiological pH. This binding caused a visual change in color, whereas no such change was noticed with other related anions (adenosine monophosphate, adenosine diphosphate, pyrophosphate, and phosphate) of biological significance. Thus, 1 x Zn could be used as a staining agent for different biological cells through binding to the ATP, generated in situ by the mitochondria (in eukaryotes). For prokaryotes (bacteria) the cell membrane takes care of the cells' energy conversion, since they lack mitochondria. ATP is produced in their unique cell structure on the cell membrane, which is not found in any eukaryotes. These stained cells could be viewed with normal light microscopy. This reagent could even be used for distinguishing the gram-positive and the gram-negative bacteria (prokaryotes). This dye was found to be nonlipophilic in nature and nontoxic to living microbes (eukaryotes and prokaryotes). Further, stained cells were found to grow in their respective media, and this confirmed the maintenance of viability of the microbes even after staining, unlike with many other dyes available commercially.
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Affiliation(s)
- Amrita Ghosh
- Central Salt and Marine Chemicals Research Institute (CSIR), Bhavnagar 364002, Gujarat, India
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82
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Hagihara S, Gremaud L, Bollot G, Mareda J, Matile S. Screening of π-Basic Naphthalene and Anthracene Amplifiers for π-Acidic Synthetic Pore Sensors. J Am Chem Soc 2008; 130:4347-51. [DOI: 10.1021/ja078256t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shinya Hagihara
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Ludovic Gremaud
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Guillaume Bollot
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jiri Mareda
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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83
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Masterson LR, Etienne MA, Porcelli F, Barany G, Hammer RP, Veglia G. Nonstereogenic alpha-aminoisobutyryl-glycyl dipeptidyl unit nucleates type I' beta-turn in linear peptides in aqueous solution. Biopolymers 2008; 88:746-53. [PMID: 17427180 DOI: 10.1002/bip.20738] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of alpha,alpha-disubstituted amino acids represents a valuable strategy to exercise conformational control in peptides. Incorporation of the nonstereogenic alpha-aminoisobutyryl-glycyl (Aib-Gly) dipeptidyl sequence into i+1 and i+2 positions of an acyclic peptide sequence, originally designed and investigated by Gellman and coworkers, [H-Arg-Tyr-Val-Glu-Val-Yyy-Xxx-Orn-Lys-Ile-Leu-Gln-NH2] nucleates a stable [2:4] left-handed type I' beta-turn in water. NMR spectra show that this newly designed beta-hairpin does not aggregate in water up to a concentration of approximately 1 mM, and that its backbone conformation is superimposable on corresponding hairpins containing the DPro-Gly (literature) and Aib-DAla (this work) sequences. The Aib-Gly turn-inducer sequence eliminates complications because of cis-trans isomerization of Zzz-Pro bonds, and constitutes an attractive alternative to the proteogenic Asn-Gly and nonproteogenic DPro-Gly motifs previously suggested as turn-inducer sequences. These design principles could be exploited to prepare water-soluble beta-hairpin peptides with robust structures and novel function.
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Affiliation(s)
- Larry R Masterson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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84
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Liu XX, Fang H, Liu Y, Zhao YF. Studies on the Contribution of Phosphoryl Group to the Non-Covalent Interaction between ATP and α-Aminophosphonic Acids Derivatives by ESI-MS and Molecular Modeling. PHOSPHORUS SULFUR 2008. [DOI: 10.1080/10426500701808168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Xiao-xia Liu
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen, P. R. China
| | - Hua Fang
- b The Third Institute of Oceanography of the State Oceanic Administration , Xiamen, P. R. China
| | - Yan Liu
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen, P. R. China
| | - Yu-fen Zhao
- a The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemistry and College of Chemistry and Chemical Engineering , Xiamen University , Xiamen, P. R. China
- c Department of Pharmacology and College of Medicine , Xiamen University , Xiamen, 361005, P. R. China
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85
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Abstract
The objective with synthetic multifunctional nanoarchitecture is to create large suprastructures with interesting functions. For this purpose, lipid bilayer membranes or conducting surfaces have been used as platforms and rigid-rod molecules as shape-persistent scaffolds. Examples for functions obtained by this approach include pores that can act as multicomponent sensors in complex matrices or rigid-rod π-stack architecture for artificial photosynthesis and photovoltaics.
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86
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Rana S, Kundu B, Durani S. A mixed-α,β miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine. Biopolymers 2007; 87:231-43. [PMID: 17879332 DOI: 10.1002/bip.20829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protein-structure space is limited to L configuration in the asymmetric alpha-amino acid structures; the function space, on other hand, seems limitless because of the chemical diversity in the amino acid side chain structures. The chemical diversity in side chain structure may be multiplied beneficially with the stereochemical diversity in main chain structure; thus, de novo protein design may be explored for customizing molecular structures stereochemically and molecular functions chemically. Illustrating de novo design in the structure space of L and D alphabet, canonical all-beta folds of poly-L structure were reprogrammed as bracelet, boat, and canoe-shaped molecules-the "boat" as a receptor-like pocket and the "canoe" as a metal-ion receptor-simply by mutating specific L-amino acid residues to the corresponding D stereochemical structure. Demonstrating customization of molecular shape stereochemically and function chemically, a 15-residue mixed-alpha, beta miniprotein of canonical poly-L structure is now reprogrammed stereochemically as a cup-shaped receptor for acetylcholine via cation-pi interaction with a triad of aromatic side chains placed in mimicry of the acetylcholine-receptor sites both natural and artificial. Evidence from CD, fluorescence, NMR, DSC, ITC, MD, and molecular-docking studies is presented to show that a rationally designed 15-residue mixed-L, D peptide is a cooperatively ordered molecular fold in the stereochemically specified molecular morphology, submicromolar in affinity of acetylcholine and thus an acetylcholine receptor exceptionally small and simple. .
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Affiliation(s)
- Soumendra Rana
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
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87
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Litvinchuk S, Tanaka H, Miyatake T, Pasini D, Tanaka T, Bollot G, Mareda J, Matile S. Synthetic pores with reactive signal amplifiers as artificial tongues. NATURE MATERIALS 2007; 6:576-80. [PMID: 17558430 DOI: 10.1038/nmat1933] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 05/10/2007] [Indexed: 05/15/2023]
Abstract
The sensation of taste is mediated by activation or deactivation of transmembrane pores. Artificial stimulus-responsive pores are enormously appealing as sensor components because changes in their activity are readily detectable in many different ways. However, the detection of multiple components in complex matrices (such as foods) with one pore sensor has so far remained elusive because the specificity necessary for sensing a target compound in complex mixtures is incompatible with the broad applicability needed for the detection of multiple components. Here, we present synthetic pores that, like our tongues, can sense flavours in food and in addition make them visibly detectable. Differential sensing and pattern recognition are solutions based on empirical and biomimetic approaches. They have been explored with synthetic receptor arrays and electronic tongues. In contrast, our approach is non-empirical as it exploits reactive amplifiers that covalently capture elusive analytes after enzymatic signal generation and drag them into synthetic pores for blockage. Reactive amplification proved to be highly sensitive and adaptable to various analytes and pores. Moreover, it can be combined with reactive filtration for minimizing interference. The system was tested on real food samples for detection of sucrose, lactose, lactate, acetate, citrate and glutamate to demonstrate the feasibility of these synthetic pores as universal sensors.
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Affiliation(s)
- Svetlana Litvinchuk
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
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88
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Rodriguez-Docampo Z, Pascu SI, Kubik S, Otto S. Noncovalent interactions within a synthetic receptor can reinforce guest binding. J Am Chem Soc 2007; 128:11206-10. [PMID: 16925439 DOI: 10.1021/ja062389h] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural and thermodynamic data are presented on the binding properties of anion receptors containing two covalently linked cyclopeptide subunits that bind sulfate and iodide anions with micromolar affinity in aqueous solution. A synchrotron X-ray crystal structure of the sulfate complex of one receptor revealed that the anion is bound between the peptide rings of the biscyclopeptide. Intimate intramolecular contacts between the nonpolar surfaces of the proline rings of the individual receptor moieties in the complex suggest that hydrophobic interactions within the receptor that do not directly involve the guest contribute to complex stability. This finding is supported by a microcalorimetric analysis of the solvent dependence of complex stability, which showed that increasing the water content of the solvent has only a weak influence on the Gibbs energy of binding. Hence, the increasing amount of energy required for desolvating the binding partners in solutions containing more water is almost compensated by the increasingly favorable hydrophobic interactions. Further observations that suggest that guest-induced intra-receptor interactions contribute to guest binding are (i) anion binding of a monomeric cyclopeptide lacking the covalent linkage between the two rings leads to the formation of 2:1 complexes; (ii) in the crystal structure of the 2:1 iodide complex of this monotopic receptor, a similar arrangement of the two cyclopeptide rings has been found as in the sulfate complex of the biscyclopeptide; (iii) complex formation of the monomeric cyclopeptide in aqueous solution is highly cooperative with a large stability constant corresponding to the formation of the 2:1 complexes from relatively instable 1:1 complexes; (iv) the monomeric cyclopeptide forms only 1:1 anion complexes in DMSO where hydrophobic interactions do not take place; and (v) introducing polar hydroxy groups on the proline rings of the monomeric cyclopeptide disrupts cooperativity causing the formation of only 1:1 complexes even in aqueous solution. Taken together these observations demonstrate that, in addition to direct receptor-substrate interactions, noncovalent interactions between the two subunits of such biscyclopeptides contribute significantly to anion complex stability. Reinforcement of molecular recognition through intra-receptor interactions should be an attractive new strategy to boost host-guest affinities.
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Affiliation(s)
- Zaida Rodriguez-Docampo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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89
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Rai R, Raghothama S, Sridharan R, Balaram P. Tuning the beta-turn segment in designed peptide beta-hairpins: construction of a stable type I' beta-turn nucleus and hairpin-helix transition promoting segments. Biopolymers 2007; 88:350-61. [PMID: 17154289 DOI: 10.1002/bip.20649] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Designed octapeptides Boc-Leu-Val-Val-Aib-(D)Xxx-Leu-Val-Val-OMe ((D)Xxx = (D)Ala, 3a;(D)Val, 3c and (D)Pro, 5a) and Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (3b) have been investigated to construct models of a stable type I' beta-turn nucleated hairpin and to generate systems for investigating helix-hairpin conformational transitions. Peptide 5a, which contains a central Aib-(D)Pro segment, is shown to adopt a stable type I' beta-turn nucleated hairpin structure, stabilized by four cross-strand hydrogen bonds. The stability of the structure in diverse solvents is established by the observation of all diagnostic NOEs expected in a beta-hairpin conformation. Replacement of (D)Pro5 by (D)Ala/(D)Val (3a-c) results in sequences that form beta-hairpins in hydrogen bonding solvents like CD(3)OH and DMSO-d(6). However, in CDCl(3) evidence for population of helical conformations is obtained. Peptide 6b (Boc-Leu-Phe-Val-Aib-Aib-Leu-Phe-Val-OMe), which contains a centrally positioned Aib-Aib segment, provides a clear example of a system, which exhibits a helical conformation in CDCl(3) and a significant population of both helices and hairpins in CD(3)OH and DMSO-d(6). The coexistence of multiple conformations is established by the simultaneous observation of diagnostic NOEs. Control over stereochemistry of the central beta-turn permits generation of models for robust beta-hairpins and also for the construction of systems that may be used to probe helix-hairpin conformational transitions.
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Affiliation(s)
- Rajkishor Rai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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90
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Bhosale R, Bhosale S, Bollot G, Gorteau V, Julliard MD, Litvinchuk S, Mareda J, Matile S, Miyatake T, Mora F, Perez-Velasco A, Sakai N, Sisson AL, Tanaka H, Tran DH. Synthetic Multifunctional Nanoarchitecture in Lipid Bilayers: Ion Channels, Sensors, and Photosystems. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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91
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Intermolecular hydrogen bonded and self-assembled β-pleated sheet structures of β-sulfidocarbonyls. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.10.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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92
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Willemse M, Janssen E, de Lange F, Wieringa B, Fransen J. ATP and FRET--a cautionary note. Nat Biotechnol 2007; 25:170-2. [PMID: 17287746 DOI: 10.1038/nbt0207-170] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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93
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Jose DA, Mishra S, Ghosh A, Shrivastav A, Mishra SK, Das A. Colorimetric sensor for ATP in aqueous solution. Org Lett 2007; 9:1979-82. [PMID: 17429979 DOI: 10.1021/ol0705797] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new chromogenic complex 1.Zn has been synthesized, and its interactions with different biologically important phosphates have been investigated in aqueous solution (pH approximately 7.2). A visual color change can be detected on binding of ATP to 1.Zn, whereas no such change is observed when other biologically related anions (AMP, ADP, PPi, or Phosphate) are used. Complex 1.Zn can also be used as a staining agent for yeast cells allowing detection under normal light microscopy.
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Affiliation(s)
- D Amilan Jose
- Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
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94
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Mahalakshmi R, Sengupta A, Raghothama S, Shamala N, Balaram P. Tryptophan rich peptides: influence of indole rings on backbone conformation. Biopolymers 2007; 88:36-54. [PMID: 17091496 DOI: 10.1002/bip.20625] [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: 11/05/2022]
Abstract
Synthetic peptides with defined secondary structure scaffolds, namely hairpins and helices, containing tryptophan residues, have been investigated in this study to probe the influence of a large number of aromatic amino acids on backbone conformations. Solution NMR investigations of Boc-W-L-W-(D)P-G-W-L-W-OMe (peptide 1), designed to form a well-folded hairpin, clearly indicates the influence of flanking aromatic residues at the (D)Pro-Gly region on both turn nucleation and strand propagation. Indole-pyrrolidine interactions in this peptide lead to the formation of the less-frequent type I' turn at the (D)Pro-Gly segment and frayed strand regions, with the strand residues adopting local helical conformations. An analog of peptide 1 with an Aib-Gly turn-nucleated hairpin (Boc-W-L-W-U-G-W-L-W-OMe (peptide 2)) shows a preference for helical structures in solution, in both chloroform and methanol. Peptides with either one (Boc-W-L-W-U-W-L-W-OMe (peptide 3)) or two (Boc-U-W-L-W-U-W-L-W-OMe (peptide 4)) helix-nucleating Aib residues give rise to the well-folded helical conformations in the chloroform solution. The results are indicative of a preference for helical folding in peptides containing a large number of Trp residues. Investigation of a tetrapeptide analog of peptide 2, Boc-W-U-G-W-OMe (peptide 5), in solution and in the crystal state (by X-ray diffraction), also indicates a preference for a helical fold. Additionally, peptide 5 is stabilized in crystals by both aromatic interactions and an array of weak interactions. Examination of Trp-rich sequences in protein structures, however, reveals no secondary structure preference, suggesting that other stabilizing interactions in a well-folded protein may offset the influence of indole rings on backbone conformations.
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95
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Woods RJ, Brower JO, Castellanos E, Hashemzadeh M, Khakshoor O, Russu WA, Nowick JS. Cyclic modular beta-sheets. J Am Chem Soc 2007; 129:2548-58. [PMID: 17295482 PMCID: PMC2597679 DOI: 10.1021/ja0667965] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of peptide beta-hairpins is problematic, because folding depends on the amino acid sequence and changes to the sequence can significantly decrease folding. Robust beta-hairpins that can tolerate such changes are attractive tools for studying interactions involving protein beta-sheets and developing inhibitors of these interactions. This paper introduces a new class of peptide models of protein beta-sheets that addresses the problem of separating folding from the sequence. These model beta-sheets are macrocyclic peptides that fold in water to present a pentapeptide beta-strand along one edge; the other edge contains the tripeptide beta-strand mimic Hao [JACS 2000, 122, 7654] and two additional amino acids. The pentapeptide and Hao-containing peptide strands are connected by two delta-linked ornithine (deltaOrn) turns [JACS 2003, 125, 876]. Each deltaOrn turn contains a free alpha-amino group that permits the linking of individual modules to form divalent beta-sheets. These "cyclic modular beta-sheets" are synthesized by standard solid-phase peptide synthesis of a linear precursor followed by solution-phase cyclization. Eight cyclic modular beta-sheets 1a-1h containing sequences based on beta-amyloid and macrophage inflammatory protein 2 were synthesized and characterized by 1H NMR. Linked cyclic modular beta-sheet 2, which contains two modules of 1b, was also synthesized and characterized. 1H NMR studies show downfield alpha-proton chemical shifts, deltaOrn delta-proton magnetic anisotropy, and NOE cross-peaks that establish all compounds but 1c and 1g to be moderately or well folded into a conformation that resembles a beta-sheet. Pulsed-field gradient NMR diffusion experiments show little or no self-association at low (=2 mM) concentrations. Changes to the residues in the Hao-containing strands of 1c and 1g improve folding and show that folding of the structures can be enhanced without altering the sequence of the pentapeptide strand. Well-folded cyclic modular beta-sheets 1a, 1b, and 1f each have a phenylalanine directly across from Hao, suggesting that cyclic modular beta-sheets containing aromatic residues across from Hao are better folded.
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Affiliation(s)
- R. Jeremy Woods
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Justin O. Brower
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Elena Castellanos
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Mehrnoosh Hashemzadeh
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Omid Khakshoor
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - Wade A. Russu
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, Phone: 949-824-6091, FAX: 949-824-9920
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96
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Tanaka H, Bollot G, Mareda J, Litvinchuk S, Tran DH, Sakai N, Matile S. Synthetic pores with sticky π-clamps. Org Biomol Chem 2007; 5:1369-80. [PMID: 17464406 DOI: 10.1039/b702255g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.
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Affiliation(s)
- Hiroyuki Tanaka
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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97
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Cheng Z, Campbell RE. Assessing the structural stability of designed beta-hairpin peptides in the cytoplasm of live cells. Chembiochem 2006; 7:1147-50. [PMID: 16810655 DOI: 10.1002/cbic.200500540] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zihao Cheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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98
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Li C, Numata M, Takeuchi M, Shinkai S. A sensitive colorimetric and fluorescent probe based on a polythiophene derivative for the detection of ATP. Angew Chem Int Ed Engl 2006; 44:6371-4. [PMID: 16173002 DOI: 10.1002/anie.200501823] [Citation(s) in RCA: 289] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chun Li
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 812-8581, Japan
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99
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Neelakandan PP, Hariharan M, Ramaiah D. Synthesis of a novel cyclic donor-acceptor conjugate for selective recognition of ATP. Org Lett 2006; 7:5765-8. [PMID: 16354061 DOI: 10.1021/ol052246k] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction and structures: see text] Novel cyclophane 1 was synthesized, and its interactions with phosphate, adenosine, AMP, ADP, and ATP have been investigated. With addition of ATP, significant decrease in absorbance of 1 was observed, whereas other guest molecules showed negligible effect. The complex between 1 and ATP was confirmed through cyclic voltammetry and 1H NMR. The uniqueness of the system is that it complexes selectively with ATP in a cavity and involves synergistic effects of both electrostatic and pi-pi stacking interactions.
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Affiliation(s)
- Prakash P Neelakandan
- Photosciences and Photonics Division, Regional Research Laboratory (CSIR), Trivandrum 695019, India
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100
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Ojida A, Nonaka H, Miyahara Y, Tamaru SI, Sada K, Hamachi I. Bis(Dpa-ZnII) Appended Xanthone: Excitation Ratiometric Chemosensor for Phosphate Anions. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200601315] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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