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Graham KA, Byrne A, Son R, Andersen NH. Reversing the typical pH stability profile of the Trp-cage. Biopolymers 2019; 110:e23260. [PMID: 30779444 DOI: 10.1002/bip.23260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022]
Abstract
The Trp-cage, an 18-20 residue miniprotein, has emerged as a primary test system for evaluating computational fold prediction and folding rate determination efforts. As it turns out, a number of stabilizing interactions in the Trp-cage folded state have a strong pH dependence; all prior Trp-cage mutants have been destabilized under carboxylate-protonating conditions. Notable among the pH dependent stabilizing interactions within the Trp-cage are: (1) an Asp as the helix N-cap, (2) an H-bonded Asp9/Arg16 salt bridge, (3) an interaction between the chain termini which are in close spatial proximity, and (4) additional side chain interactions with Asp9. In the present study, we have prepared Trp-cage species that are significantly more stable at pH 2.5 (rather than 7) and quantitated the contribution of each interaction listed above. The Trp-cage structure remains constant with the pH change. The study has also provided measures of the stabilizing contribution of indole ring shielding from surface exposure and the destabilizing effects of an ionized Asp at the C-terminus of an α-helix.
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Affiliation(s)
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Ruth Son
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington
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2
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Yousuf I, Usman M, Ahmad M, Tabassum S, Arjmand F. Single X-ray crystal structure, DFT studies and topoisomerase I inhibition activity of a tailored ionic Ag( i) nalidixic acid–piperazinium drug entity specific for pancreatic cancer cells. NEW J CHEM 2018; 42:506-519. [DOI: 10.1039/c7nj03602g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
DFT studies, Topo I inhibition assay and cytotoxic activity of novel ionic Ag(i) nalidixic acid–piperazinium molecular entity.
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Affiliation(s)
- Imtiyaz Yousuf
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Mohammad Usman
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Musheer Ahmad
- Department of Applied Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Sartaj Tabassum
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Farukh Arjmand
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
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3
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Zhang W, Yang H, Liu F, Chen T, Hu G, Guo D, Hou Q, Wu X, Su Y, Wang J. Molecular interactions between DOPA and surfaces with different functional groups: a chemical force microscopy study. RSC Adv 2017. [DOI: 10.1039/c7ra04228k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The adhesion of mussel foot proteins (Mfps) to a variety of surfaces has been widely investigated, but the mechanisms behind the mussel adhesion to surfaces with different properties are far from being understood.
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4
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Konda M, Bhowmik S, Mobin SM, Biswas S, Das AK. Modulating Hydrogen Bonded Self-assembled Patterns and Morphological Features by a Change in Side Chain of Third Amino Acid of Synthetic γ- Amino Acid Based Tripeptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Soumitra Bhowmik
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Shaikh M. Mobin
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
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5
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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6
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Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Phys Chem Chem Phys 2015; 16:9876-91. [PMID: 24419903 DOI: 10.1039/c3cp52774c] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
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Affiliation(s)
- R Chaudret
- Sorbonne Universités, UPMC, Laboratoire de Chimie Théorique and CNRS, UMR 7616, 75252 Paris Cedex 05, Paris, France.
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7
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Zehnacker A. Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies. INT REV PHYS CHEM 2014. [DOI: 10.1080/0144235x.2014.911548] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Lovas S, Zhang Y, Yu J, Lyubchenko YL. Molecular mechanism of misfolding and aggregation of Aβ(13-23). J Phys Chem B 2013; 117:6175-86. [PMID: 23642026 DOI: 10.1021/jp402938p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The misfolding and self-assembly of the amyloid-beta (Aβ) peptide into aggregates is a molecular signature of the development of Alzheimer's disease, but molecular mechanisms of the peptide aggregation remain unknown. Here, we combined Atomic Force Microscopy (AFM) and Molecular Dynamics (MD) simulations to characterize the misfolding process of an Aβ peptide. Dynamic force spectroscopy AFM analysis showed that the peptide forms stable dimers with a lifetime of ∼1 s. During MD simulations, isolated monomers gradually adopt essentially similar nonstructured conformations independent from the initial structure. However, when two monomers approach their structure changes dramatically, and the conformational space for the two monomers become restricted. The arrangement of monomers in antiparallel orientation leads to the cooperative formation of β-sheet conformation. Interactions, including hydrogen bonds, salt bridges, and weakly polar interactions of side chains stabilize the structure of the dimer. Under the applied force, the dimer, as during the AFM experiments, dissociates in a cooperative manner. Thus, misfolding of the Aβ peptide proceeds via the loss of conformational flexibility and formation of stable dimers suggesting their key role in the subsequent Aβ aggregation process.
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Affiliation(s)
- Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States.
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9
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Palermo NY, Thomas P, Murphy RF, Lovas S. Hexapeptide fragment of carcinoembryonic antigen which acts as an agonist of heterogeneous ribonucleoprotein M. J Pept Sci 2012; 18:252-60. [PMID: 22392880 DOI: 10.1002/psc.2393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 12/08/2011] [Accepted: 12/12/2011] [Indexed: 12/15/2022]
Abstract
Colorectal cancers with metastatic potential secrete the glycoprotein carcinoembryonic antigen (CEA). CEA has been implicated in colorectal cancer metastasis by inducing Kupffer cells to produce inflammatory cytokines which, in turn, make the hepatic micro-environment ideal for tumor cell implantation. CEA binds to the heterogeneous ribonucleoprotein M (hnRNP M) which acts as a cell surface receptor in Kupffer cells. The amino acid sequence in CEA, which binds the hnRNP M receptor, is Tyr-Pro-Glu-Leu-Pro-Lys. In this study, the structure of Ac-Tyr-Pro-Glu-Leu-Pro-Lys-NH₂ (YPELPK) was investigated using electronic circular dichroism, vibrational circular dichroism, and molecular dynamics simulations. The binding of the peptide to hnRNP M was also investigated using molecular docking calculations. The biological activity of YPELPK was studied using differentiated human THP-1 cells, which express hnRNP M on their surface and secrete IL-6 when stimulated by CEA. YPELPK forms a stable polyproline-II helix and stimulates IL-6 production of THP-1 cells at micromolar concentrations.
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Affiliation(s)
- Nicholas Y Palermo
- Departments of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
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10
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Rovó P, Farkas V, Hegyi O, Szolomájer-Csikós O, Tóth GK, Perczel A. Cooperativity network of Trp-cage miniproteins: probing salt-bridges. J Pept Sci 2011; 17:610-9. [DOI: 10.1002/psc.1377] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/18/2011] [Accepted: 03/24/2011] [Indexed: 11/06/2022]
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11
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The square conformation of phenylglycine-incorporated ascidiacyclamide is stabilized by CH/π interactions between amino acid side chains. Bioorg Med Chem 2011; 19:3372-7. [DOI: 10.1016/j.bmc.2011.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/14/2011] [Accepted: 04/18/2011] [Indexed: 11/20/2022]
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12
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Hatfield MPD, Murphy RF, Lovas S. The CLN025 decapeptide retains a β-hairpin conformation in urea and guanidinium chloride. J Phys Chem B 2011; 115:4971-81. [PMID: 21480621 DOI: 10.1021/jp111076j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The conformational stability of the β-hairpin miniprotein, CLN025, a variant of chignolin in which the N- and C-terminal glycines are replaced by tyrosines, in various concentrations of guanidinium chloride (GdmCl) and urea was examined by molecular dynamics simulations and electronic circular dichroism (ECD) spectropolarimetry. The peptide maintains its β-hairpin conformation in GdmCl and urea solutions. In GdmCl, Gly7 influences the turn to reduce the number of Asp3-Gly7 H-bonds and the Tyr1-Trp9 H-bond is lost. The structure of the peptide is less stable in 3 M GdmCl than in water or 6 M GdmCl, because the number of Asp3-Thr8 and Tyr1-Tyr10 H-bonds are reduced and the Tyr2 side chain moves away from the Pro4 and Trp9 side chains and toward the Tyr10 side chain. This reduces the number of Tyr2-Pro4 CH-π interactions and Tyr2-Trp9 and Tyr1-Tyr10 aromatic-aromatic (Ar-Ar) interactions and increases the number of Tyr2-Tyr10 Ar-Ar interactions. In 6 M GdmCl at 300 and 333 K, the number of Tyr1-Tyr10 and Asp3-Thr8 H-bonds increases, but fewer structures have Tyr2-Pro4 CH-π and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In urea, Gly7 is in a mixture of β-turn and random meander structures and the number of Asp3-Thr6 and Tyr1-Tyr10 H-bonds are reduced as are the number of Tyr2-Pro4 CH-π interactions and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In 4 M urea, a shorter turn places Gly7 into the β-sheet region and Tyr10 is pushed out into the solvent. In 8 M urea, the number of Asp3-Glu5 H-bonds is increased and the β-sheet is lost, but the electrostatic interaction between the charged termini is restored and a cation-π interaction between the indolyl ring of Trp9 and the positively charged N-terminus is formed. In 8 M urea at 333 K, the β-hairpin conformation is almost lost. The structure of CLN025 is stable, because the weakly polar interactions and H-bonds maintain the β-hairpin conformation in the various environments. CLN025 should not be considered a miniprotein, because it lacks a well-defined tertiary structure, it is resistant to denaturation, it does not have an increased heat capacity near its melting temperature, and the structures near and above the melting temperature retain a β-hairpin conformation.
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Affiliation(s)
- Marcus P D Hatfield
- Department of Biomedical Sciences, Criss II, Room 313, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
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13
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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14
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Scuderi D, Le Barbu-Debus K, Zehnacker A. The role of weak hydrogen bonds in chiral recognition. Phys Chem Chem Phys 2011; 13:17916-29. [DOI: 10.1039/c1cp20987f] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Hatfield MPD, Murphy RF, Lovas S. VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents. Biopolymers 2010; 93:442-50. [PMID: 19937759 PMCID: PMC4499852 DOI: 10.1002/bip.21356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.
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Affiliation(s)
| | - Richard. F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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Hatfield MPD, Murphy RF, Lovas S. Molecular dynamics analysis of the conformations of a beta-hairpin miniprotein. J Phys Chem B 2010; 114:3028-37. [PMID: 20148510 PMCID: PMC2848447 DOI: 10.1021/jp910465e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations of a beta-hairpin miniprotein, CLN025, were performed to examine the conformational stability of the peptide in H(2)O at 278, 300, 333, and 363 K, as well as in TFE, MeOH, and DMSO at 300 K. CLN025 is a variant of the Chignolin miniprotein, in which the terminal Gly residues of Chignolin are replaced with Tyr residues, which leads to a 29.7 K increase in melting temperature. The energy of the intramolecular interactions was calculated using DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. CLN025 maintained a beta-hairpin conformation in all environments. The beta-hairpin is stabilized by hydrogen bonds, an electrostatic interaction between the charged termini of the peptide, and weakly polar interactions. The interaction between the backbones of the N and C-terminal strands accounts for -97.32 to -120.87 kcal mol(-1) of the stabilization energy. The energies of the CH-pi interactions between Tyr2 and Pro4 were between -1.80 and -8.9 kcal mol(-1), and the energy of the Tyr2-Trp9 Ar-Ar interaction was between -0.43 and -8.11 kcal mol(-1). Increasing temperature caused the Tyr2-Pro4 CH-pi and the Tyr2-Trp9 and Tyr2-Tyr10 Ar-Ar interactions to become less favorable, but the Tyr1-Trp9 interaction became more favorable and played an important role in stabilizing the beta-hairpin of CLN025 that resulted in the increased melting temperature. Weakly polar interactions play an important role in the structure and stability of CLN025 and other proteins.
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Affiliation(s)
| | - Richard F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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17
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Yin XB, Zhang YJ, Fang ZY, Xu ZY. Hydrothermal Synthesis of Rhombus-like SmCO 3OH Microplates and Its Photoluminescence Property Doped with Eu 3+. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/01/102-106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Fan W, Zeng J, Zhang R. Quantum Mechanical Quantification of Weakly Interacting Complexes of Peptides with Single-Walled Carbon Nanotubes. J Chem Theory Comput 2009; 5:2879-85. [DOI: 10.1021/ct9002493] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenjie Fan
- Centre of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China, MedChemSoft Solutions, P.O. Box 5143, Wantirna South, VIC 3152, Australia, and College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jun Zeng
- Centre of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China, MedChemSoft Solutions, P.O. Box 5143, Wantirna South, VIC 3152, Australia, and College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Ruiqin Zhang
- Centre of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China, MedChemSoft Solutions, P.O. Box 5143, Wantirna South, VIC 3152, Australia, and College of Chemistry, Sichuan University, Chengdu 610064, China
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19
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Ottiger P, Pfaffen C, Leist R, Leutwyler S, Bachorz RA, Klopper W. Strong N−H···π Hydrogen Bonding in Amide−Benzene Interactions. J Phys Chem B 2009; 113:2937-43. [DOI: 10.1021/jp8110474] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philipp Ottiger
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Chantal Pfaffen
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Roman Leist
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie and Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Rafał A. Bachorz
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
| | - Wim Klopper
- Center for Functional Nanostructures (CFN) and Institut für Physikalische Chemie, UniversitätKarlsruhe (TH), D-76128 Karlsruhe, Germany
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20
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Csontos J, Murphy RF, Lovas S. The role of weakly polar and H-bonding interactions in the stabilization of the conformers of FGG, WGG, and YGG: an aqueous phase computational study. Biopolymers 2008; 89:1002-11. [PMID: 18615659 DOI: 10.1002/bip.21049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The energetics of intramolecular interactions on the conformational potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG), and N-Ac-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-cc-pVTZ level of theory. In the global minima, 10%, 31%, and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG, and YGG. In the prominent cases 46%, 62%, and 46% of the stabilization energy is from the weakly polar interactions, respectively, in FGG, WGG, and YGG. On average, weakly polar interactions account for 15%, 34%, and 9% of the stabilization energies of the FGG, WGG, and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function.
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Affiliation(s)
- József Csontos
- Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, NE 68178, USA
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