1
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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2
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Abril D, Ferrer V, Mirabal-Gallardo Y, Cabrera-Barjas G, Segura C, Marican A, Pereira A, Durán-Lara EF, Valdés O. Comparative Study of Three Dyes' Adsorption onto Activated Carbon from Chenopodium quinoa Willd and Quillaja saponaria. MATERIALS 2022; 15:ma15144898. [PMID: 35888365 PMCID: PMC9321238 DOI: 10.3390/ma15144898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022]
Abstract
The present study shows porous activated carbon obtained from Chenopodium quinoa Willd and Quillaja saponaria and their use as potential adsorbents to remove three types of dyes from aqueous solutions. The adsorption results were compared with commercial charcoal to check their efficiency. All porous carbon materials were activated using carbon dioxide and steam and fully characterized. Moreover, the steam-activated samples exhibited a high total pore volume with a BET surface area of around 800 m2 g−1. Batch adsorption experiments showed that commercial charcoal is the charcoal that offered the best adsorption efficiency for tartrazine and sunset yellow FCF. However, in the case of crystal violet, all activated carbons obtained from Chenopodium quinoa Willd and Quillaja saponaria showed the best captures, outperforming commercial charcoal. Molecular dockings of the dyes on the commercial charcoal surface were performed using AutoDock Vina. The kinetic results of the three isotherm’s models for the present data follow the order: Langmuir~Freundlich > Temkin.
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Affiliation(s)
- Diana Abril
- Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca 3460000, Chile;
| | - Victor Ferrer
- Unidad de Desarrollo Tecnológico, UDT, Universidad de Concepción, Av. Cordillera 2634, Parque Industrial Coronel, Coronel 4190000, Chile; (V.F.); (G.C.-B.); (C.S.)
- Centro Nacional de Excelencia para la Industria de la Madera (CENAMAD), Pontificia Universidad Católica de Chile, Av. Vicuña Mackena 4860, Santiago 7820436, Chile
| | - Yaneris Mirabal-Gallardo
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería Civil, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile;
| | - Gustavo Cabrera-Barjas
- Unidad de Desarrollo Tecnológico, UDT, Universidad de Concepción, Av. Cordillera 2634, Parque Industrial Coronel, Coronel 4190000, Chile; (V.F.); (G.C.-B.); (C.S.)
- Centro Nacional de Excelencia para la Industria de la Madera (CENAMAD), Pontificia Universidad Católica de Chile, Av. Vicuña Mackena 4860, Santiago 7820436, Chile
| | - Cristina Segura
- Unidad de Desarrollo Tecnológico, UDT, Universidad de Concepción, Av. Cordillera 2634, Parque Industrial Coronel, Coronel 4190000, Chile; (V.F.); (G.C.-B.); (C.S.)
| | - Adolfo Marican
- Instituto de Química de Recursos Naturales, Universidad de Talca, Talca 3460000, Chile; (A.M.); (A.P.)
| | - Alfredo Pereira
- Instituto de Química de Recursos Naturales, Universidad de Talca, Talca 3460000, Chile; (A.M.); (A.P.)
| | - Esteban F. Durán-Lara
- Bio & NanoMaterials Laboratory, Drug Delivery and Controlled Release, Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca 3460000, Chile;
| | - Oscar Valdés
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca 3460000, Chile
- Correspondence:
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3
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Abstract
A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Wang J, Shao L, Yan P, Liu C, Liu X, Zhang XM. Are solvent effects important for intramolecular C—H···O
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hydrogen bonding interactions? J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jinhu Wang
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Linjun Shao
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals ProcessShaoxing University Shaoxing China
| | - Peng Yan
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Chunli Liu
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Xuejing Liu
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
| | - Xian M. Zhang
- College of Chemistry, Chemical Engineering and Material ScienceZaozhuang University Zaozhuang China
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5
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Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry 2016; 55:6056-6069. [PMID: 27753291 DOI: 10.1021/acs.biochem.6b00624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.
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Affiliation(s)
- Karan Kapoor
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
| | - Michael R Duff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Amit Upadhyay
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States
| | - Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Arnold M Saxton
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Elizabeth E Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
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6
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Adhikari U, Scheiner S. First steps in growth of a polypeptide toward β-sheet structure. J Phys Chem B 2013; 117:11575-83. [PMID: 24028425 DOI: 10.1021/jp406326h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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Abstract
Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.
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8
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JC virus agnoprotein enhances large T antigen binding to the origin of viral DNA replication: evidence for its involvement in viral DNA replication. Virology 2012; 433:12-26. [PMID: 22840425 DOI: 10.1016/j.virol.2012.06.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/25/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
Agnoprotein is required for the successful completion of the JC virus (JCV) life cycle and was previously shown to interact with JCV large T-antigen (LT-Ag). Here, we further characterized agnoprotein's involvement in viral DNA replication. Agnoprotein enhances the DNA binding activity of LT-Ag to the viral origin (Ori) without directly interacting with DNA. The predicted amphipathic α-helix of agnoprotein plays a major role in this enhancement. All three phenylalanine (Phe) residues of agnoprotein localize to this α-helix and Phe residues in general are known to play critical roles in protein-protein interaction, protein folding and stability. The functional relevance of all Phe residues was investigated by mutagenesis. When all were mutated to alanine (Ala), the mutant virus (F31AF35AF39A) replicated significantly less efficiently than each individual Phe mutant virus alone, indicating the importance of Phe residues for agnoprotein function. Collectively, these studies indicate a close involvement of agnoprotein in viral DNA replication.
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9
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Philip V, Harris J, Adams R, Nguyen D, Spiers J, Baudry J, Howell EE, Hinde RJ. A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs. Biochemistry 2011; 50:2939-50. [PMID: 21366334 DOI: 10.1021/bi200066k] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.
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Affiliation(s)
- Vivek Philip
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, United States
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10
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de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL. Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins. J Theor Biol 2010; 271:136-44. [PMID: 21130100 DOI: 10.1016/j.jtbi.2010.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/03/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
Abstract
A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools.
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Affiliation(s)
- Miguel M de Sousa
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Cristian R Munteanu
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal; Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Alejandro Pazos
- Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Nuno A Fonseca
- CRACS-INESC Porto L.A., R. Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - Rui Camacho
- LIAAD-INESC-Porto, DEI and FEUP, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - A L Magalhães
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
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11
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Cheng RP, Girinath P, Suzuki Y, Kuo HT, Hsu HC, Wang WR, Yang PA, Gullickson D, Wu CH, Koyack MJ, Chiu HP, Weng YJ, Hart P, Kokona B, Fairman R, Lin TE, Barrett O. Positional Effects on Helical Ala-Based Peptides. Biochemistry 2010; 49:9372-84. [DOI: 10.1021/bi101156j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Prashant Girinath
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yuta Suzuki
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Chun Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Donald Gullickson
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Cheng-Hsun Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Marc J. Koyack
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yi-Jen Weng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Tzu-En Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Olivia Barrett
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
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12
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Mokrab Y, Stevens TJ, Mizuguchi K. Lipophobicity and the residue environments of the transmembrane α-helical bundle. Proteins 2008; 74:32-49. [DOI: 10.1002/prot.22130] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Hanshaw RG, Stahelin RV, Smith BD. Noncovalent keystone interactions controlling biomembrane structure. Chemistry 2008; 14:1690-7. [PMID: 18085538 DOI: 10.1002/chem.200701589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a biomedical need to develop molecular recognition systems that selectively target the interfaces of protein and lipid aggregates in biomembranes. This is an extremely challenging problem in supramolecular chemistry because the biological membrane is a complex dynamic assembly of multifarious molecular components with local inhomogeneity. Two simplifying concepts are presented as a framework for basing molecular design strategies. The first generalization is that association of two binding partners in a biomembrane will be dominated by one type of non-covalent interaction which is referred to as the keystone interaction. Structural mutations in membrane proteins that alter the strength of this keystone interaction will likely have a major effect on biological activity and often will be associated with disease. The second generalization is to view the structure of a cell membrane as three spatial regions, that is, the polar membrane surface, the midpolar interfacial region and the non-polar membrane interior. Each region has a distinct dielectric, and the dominating keystone interaction between binding partners will be different. At the highly polar membrane surface, the keystone interactions between charged binding partners are ion-ion and ion-dipole interactions; whereas, ion-dipole and ionic hydrogen bonding are very influential at the mid-polar interfacial region. In the non-polar membrane interior, van der Waals forces and neutral hydrogen bonding are the keystone interactions that often drive molecular association. Selected examples of lipid and transmembrane protein association systems are described to illustrate how the association thermodynamics and kinetics are dominated by these keystone noncovalent interactions.
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Affiliation(s)
- Roger G Hanshaw
- Department of Chemistry and Biochemistry and Walther Cancer Center, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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14
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Stability and Design of α-Helical Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:1-52. [DOI: 10.1016/s0079-6603(08)00601-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Scheiner S, Kar T. Effect of solvent upon CH...O hydrogen bonds with implications for protein folding. J Phys Chem B 2007; 109:3681-9. [PMID: 16851407 DOI: 10.1021/jp0446736] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The series of CH...O bonds formed between CF(n)H(4-n) (n = 0-3) and water are studied by quantum calculations under vacuum and in various solvents, including aqueous environment. The results are compared with the OH...O bond of the water dimer in the same solvents. Increasing polarity of the solvent leads in all cases to a lessening of the H-bond interaction energy, in a uniform fashion such that the CH...O bonds all remain weaker than OH...O in any solvent. These H-bond weakenings are coupled to a shortening of the inter-subunit separation. The contraction of the covalent CH bond to the bridging proton is reduced as the solvent becomes more polar, and the blue shift of its stretching vibration is likewise diminished. A process is considered that simulates protein folding by starting from a pair of noninteracting subunits in aqueous solvent and then goes to a H-bonded pair within the confines of a protein environment. This process is found to be energetically more favorable for some of the CH...O H-bonds than for the nominally stronger conventional OH...O H-bond. This finding suggests that CH...O bonds can make important energetic contributions to protein folding, on par with those made by traditional H-bonds.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
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16
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Guo H, Beahm RF, Guo H. Stabilization and Destabilization of the Cδ−H···OC Hydrogen Bonds Involving Proline Residues in Helices. J Phys Chem B 2004. [DOI: 10.1021/jp0480192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haobo Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Robert F. Beahm
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996
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17
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Abstract
Aromatic interactions, including pi-pi, cation-pi, aryl-sulfur, and carbohydrate-pi interactions, have been shown to be prevalent in proteins through protein structure analysis, suggesting that they are important contributors to protein structure. However, the magnitude and significance of aromatic interactions is not defined by such studies. Investigation of aromatic interactions in the context of structured peptides has complemented studies of protein structure and has provided a wealth of information regarding the role of aromatic interactions in protein structure and function. Recent advances in this area are reviewed.
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Affiliation(s)
- Marcey L Waters
- Department of Chemistry, CB 3290, University of North Carolina, Chapel Hill, NC 27599, USA
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Lear JD, Stouffer AL, Gratkowski H, Nanda V, Degrado WF. Association of a model transmembrane peptide containing gly in a heptad sequence motif. Biophys J 2004; 87:3421-9. [PMID: 15315956 PMCID: PMC1304808 DOI: 10.1529/biophysj.103.032839] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A peptide containing glycine at a and d positions of a heptad motif was synthesized to investigate the possibility that membrane-soluble peptides with a Gly-based, left-handed helical packing motif would associate. Based on analytical ultracentrifugation in C14-betaine detergent micelles, the peptide did associate in a monomer-dimer equilibrium, although the association constant was significantly less than that reported for the right-handed dimer of the glycophorin A transmembrane peptide in similar detergents. Fluorescence resonance energy transfer (FRET) experiments conducted on peptides labeled at their N-termini with either tetramethylrhodamine (TMR) or 7-nitrobenz-2-oxa-1,3-diazole (NBD) also indicated association. However, analysis of the FRET data using the usual assumption of complete quenching for NBD-TMR pairs in the dimer could not be quantitatively reconciled with the analytical ultracentrifugation-measured dimerization constant. This led us to develop a general treatment for the association of helices to either parallel or antiparallel structures of any aggregation state. Applying this treatment to the FRET data, constraining the dimerization constant to be within experimental uncertainty of that measured by analytical ultracentrifugation, we found the data could be well described by a monomer-dimer equilibrium with only partial quenching of the dimer, suggesting that the helices are most probably antiparallel. These results also suggest that a left-handed Gly heptad repeat motif can drive membrane helix association, but the affinity is likely to be less strong than the previously reported right-handed motif described for glycophorin A.
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Affiliation(s)
- James D Lear
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Abstract
Cation-pi interactions between aromatic amino acids and the positively charged residues lysine and arginine have been proposed to play an important role in stabilizing protein structure. We have used a peptide that adopts a coiled coil structure as a model system to evaluate the energetic contribution of cation-pi interactions to protein folding. Peptides were designed in which phenylalanine, tyrosine, and tryptophan were placed at a solvent-exposed position of the helix, one turn removed from an arginine residue that could provide a favorable cation-pi interaction. Only the arginine-phenylalanine pairing provided significant stabilization of the peptide structure and it appears that hydrophobic packing, rather than the cation-pi effect, is more likely to be responsible for the stability of this peptide. We conclude that any stabilizing effect of cation-pi interactions in these peptides is much smaller than that predicted from computational studies.
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Affiliation(s)
- Morris M Slutsky
- Department of Chemistry and Division of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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