1
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Roseli RB, Huang YH, Henriques ST, Kaas Q, Craik DJ. Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184268. [PMID: 38191035 DOI: 10.1016/j.bbamem.2023.184268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Kalata B1 (kB1), a naturally occurring cyclotide has been shown experimentally to bind lipid membranes that contain phosphatidylethanolamine (PE) phospholipids. Here, molecular dynamics simulations were used to explore its interaction with two phospholipids, palmitoyloleoylphosphatidylethanolamine (POPE), palmitoyloleoylphosphatidylcholine (POPC), and a heterogeneous membrane comprising POPC/POPE (90:10), to understand the basis for the selectivity of kB1 towards PE phospholipids. The simulations showed that in the presence of only 10 % POPE lipid, kB1 forms a stable binding complex with membrane bilayers. An ionic interaction between the E7 carboxylate group of kB1 and the ammonium group of PE headgroups consistently initiates binding of kB1 to the membrane. Additionally, stable noncovalent interactions such as hydrogen bonding (E7, T8, V10, G11, T13 and N15), cation-π (W23), and CH-π (W23) interactions between specific residues of kB1 and the lipid membrane play an important role in stabilizing the binding. These findings are consistent with a structure-activity relationship study on kB1 where lysine mutagenesis on the bioactive and hydrophobic faces of the peptide abolished membrane-dependent bioactivities. In summary, our simulations suggest the importance of residue E7 (in the bioactive face) in enabling kB1 to recognize and bind selectively to PE-containing phospholipids bilayers through ionic and hydrogen bonding interactions, and of W23 (in the hydrophobic face) for the association and insertion of kB1 into the lipid bilayer through cation-π and CH-π interactions. Overall, this work enhances our understanding of the molecular basis of the membrane binding and bioactivity of this prototypic cyclotide.
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Affiliation(s)
- Ras Baizureen Roseli
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia.
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2
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Straus SK. Tryptophan- and arginine-rich antimicrobial peptides: Anti-infectives with great potential. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184260. [PMID: 38113954 DOI: 10.1016/j.bbamem.2023.184260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
With the increasing prevalence of multidrug resistant (MDR) bacteria, there is a need to design synthetic antimicrobial peptides (AMPs) that are effective and selective for bacteria, i.e. non-toxic to mammalian cells. One design strategy, namely the use of tryptophan- and arginine-rich AMPs, is rooted in the study of natural AMPs that are composed mainly of these amino acids, such as lactoferricin, tritrpticin, and puroindoline. A number of important studies on these AMPs by the Vogel group are reviewed here. More recent work on W-/R-rich peptides is also presented. The examples show that these peptides represent anti-infectives with great potential.
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Affiliation(s)
- Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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3
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Sam S, Sung S, Kim D. Sensitive Detection of Biomolecular Adsorption by a Low-Density Surfactant Layer Using Sum-Frequency Vibrational Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17412-17419. [PMID: 38050679 DOI: 10.1021/acs.langmuir.3c02546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Small molecules or proteins interact with a biomembrane in various ways for molecular recognition, structure stabilization, and transmembrane signaling. In this study, 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP), having a choline group, was used to investigate this interaction by using sum-frequency vibrational spectroscopy. The sum-frequency spectrum characteristic of a neat monolayer changed to that of a bare air/water interface at a larger molecular area of the DPTAP molecules due to local laser heating. Upon introduction of the aromatic molecules in the subphase at around 120 Å2 per molecule, the sum-frequency signal suddenly reappeared due to molecular adhesion, and this was utilized to probe the adsorption of the aromatic ring molecules in the water subphase to the choline headgroup of the DPTAP by cation-π interaction. The onset concentrations of this sum-frequency signal change allowed a comparison of the relative interaction strengths between different aromatic molecules. A zwitterionic surfactant molecule (DPPC) was found to interact weakly compared to the cationic DPTAP molecule.
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Affiliation(s)
- Sokhuoy Sam
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
| | - Siheon Sung
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
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4
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Mitchell W, Tamucci JD, Ng EL, Liu S, Birk AV, Szeto HH, May ER, Alexandrescu AT, Alder NN. Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds. eLife 2022; 11:75531. [PMID: 35913044 PMCID: PMC9342957 DOI: 10.7554/elife.75531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria play a central role in metabolic homeostasis, and dysfunction of this organelle underpins the etiology of many heritable and aging-related diseases. Tetrapeptides with alternating cationic and aromatic residues such as SS-31 (elamipretide) show promise as therapeutic compounds for mitochondrial disorders. In this study, we conducted a quantitative structure-activity analysis of three alternative tetrapeptide analogs, benchmarked against SS-31, that differ with respect to aromatic side chain composition and sequence register. We present the first structural models for this class of compounds, obtained with Nuclear Magnetic Resonance (NMR) and molecular dynamics approaches, showing that all analogs except for SS-31 form compact reverse turn conformations in the membrane-bound state. All peptide analogs bound cardiolipin-containing membranes, yet they had significant differences in equilibrium binding behavior and membrane interactions. Notably, analogs had markedly different effects on membrane surface charge, supporting a mechanism in which modulation of membrane electrostatics is a key feature of their mechanism of action. The peptides had no strict requirement for side chain composition or sequence register to permeate cells and target mitochondria in mammalian cell culture assays. All four peptides were pharmacologically active in serum withdrawal cell stress models yet showed significant differences in their abilities to restore mitochondrial membrane potential, preserve ATP content, and promote cell survival. Within our peptide set, the analog containing tryptophan side chains, SPN10, had the strongest impact on most membrane properties and showed greatest efficacy in cell culture studies. Taken together, these results show that side chain composition and register influence the activity of these mitochondria-targeted peptides, helping provide a framework for the rational design of next-generation therapeutics with enhanced potency.
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Affiliation(s)
- Wayne Mitchell
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jeffrey D Tamucci
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Emery L Ng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Shaoyi Liu
- Social Profit Network, Menlo Park, CA, United States
| | - Alexander V Birk
- Department of Biology, York College of CUNY, New York, NY, United States
| | - Hazel H Szeto
- Social Profit Network, Menlo Park, CA, United States
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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5
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de Araujo AD, Hoang HN, Lim J, Mak JYW, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022; 61:e202203995. [PMID: 35523729 PMCID: PMC9543247 DOI: 10.1002/anie.202203995] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 11/30/2022]
Abstract
Aromatic groups are key mediators of protein–membrane association at cell surfaces, contributing to hydrophobic effects and π‐membrane interactions. Here we show electrostatic and hydrophobic influences of aromatic ring substituents on membrane affinity and cell uptake of helical, cyclic and cell penetrating peptides. Hydrophobicity is important, but subtle changes in electrostatic surface potential, dipoles and polarizability also enhance association with phospholipid membranes and cell uptake. A combination of fluorine and sulfur substituents on an aromatic ring induces microdipoles that enhance cell uptake of 12‐residue peptide inhibitors of p53‐HDM2 interaction and of cell‐penetrating cyclic peptides. These aromatic motifs can be readily inserted into peptide sidechains to enhance their cell uptake.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Jeffrey Y. W. Mak
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology ARC Centre of Excellence for Innovations in Peptide & Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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6
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Herrera-León C, Ramos-Martín F, El Btaouri H, Antonietti V, Sonnet P, Martiny L, Zevolini F, Falciani C, Sarazin C, D’Amelio N. The Influence of Short Motifs on the Anticancer Activity of HB43 Peptide. Pharmaceutics 2022; 14:pharmaceutics14051089. [PMID: 35631675 PMCID: PMC9147034 DOI: 10.3390/pharmaceutics14051089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 01/10/2023] Open
Abstract
Despite the remarkable similarity in amino acid composition, many anticancer peptides (ACPs) display significant differences in terms of activity. This strongly suggests that particular relative dispositions of amino acids (motifs) play a role in the interaction with their biological target, which is often the cell membrane. To better verify this hypothesis, we intentionally modify HB43, an ACP active against a wide variety of cancers. Sequence alignment of related ACPs by ADAPTABLE web server highlighted the conserved motifs that could be at the origin of the activity. In this study, we show that changing the order of amino acids in such motifs results in a significant loss of activity against colon and breast cancer cell lines. On the contrary, amino acid substitution in key motifs may reinforce or weaken the activity, even when the alteration does not perturb the amphipathicity of the helix formed by HB43 on liposomes mimicking their surface. NMR and MD simulations with different membrane models (micelles, bicelles, and vesicles) indicate that the activity reflects the insertion capability in cancer-mimicking serine-exposing membranes, supported by the insertion of N-terminal phenylalanine in the FAK motif and the anchoring to the carboxylate of phosphatidylserine by means of arginine side chains.
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Affiliation(s)
- Claudia Herrera-León
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (F.R.-M.); (C.S.)
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (F.R.-M.); (C.S.)
| | - Hassan El Btaouri
- Matrice Extracellulaire et Dynamique Cellulaire UMR 7369 CNRS, Université de Reims Champagne Ardenne (URCA), 51100 Reims, France; (H.E.B.); (L.M.)
| | - Viviane Antonietti
- Agents Infectieux, Résistance et Chimiothérapie, AGIR UR 4294, Université de Picardie Jules Verne, UFR de Pharmacie, 80037 Amiens, France; (V.A.); (P.S.)
| | - Pascal Sonnet
- Agents Infectieux, Résistance et Chimiothérapie, AGIR UR 4294, Université de Picardie Jules Verne, UFR de Pharmacie, 80037 Amiens, France; (V.A.); (P.S.)
| | - Laurent Martiny
- Matrice Extracellulaire et Dynamique Cellulaire UMR 7369 CNRS, Université de Reims Champagne Ardenne (URCA), 51100 Reims, France; (H.E.B.); (L.M.)
| | - Fabrizia Zevolini
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy; (F.Z.); (C.F.)
| | - Chiara Falciani
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy; (F.Z.); (C.F.)
| | - Catherine Sarazin
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (F.R.-M.); (C.S.)
| | - Nicola D’Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, 80039 Amiens, France; (C.H.-L.); (F.R.-M.); (C.S.)
- Correspondence: ; Tel.: +33-3-22-82-74-73; Fax: +33-3-22-82-75
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7
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de Araujo AD, Hoang HN, Lim J, Mak J, Fairlie DP. Tuning Electrostatic and Hydrophobic Surfaces of Aromatic Rings to Enhance Membrane Association and Cell Uptake of Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aline Dantes de Araujo
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Huy N Hoang
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Junxian Lim
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - Jeffrey Mak
- The University of Queensland Institute for Molecular Bioscience Institute for Molecular Bioscience Institute for Molecular Bioscience, The University of Queensland 4072 Brisbane AUSTRALIA
| | - David P Fairlie
- Institute for Molecular Bioscience Division of Chemistry and Structural Biology The University of Queensland 4072 Brisbane AUSTRALIA
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8
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Tan R, Wang M, Xu H, Qin L, Wang J, Cui P, Ru S. Improving the Activity of Antimicrobial Peptides Against Aquatic Pathogen Bacteria by Amino Acid Substitutions and Changing the Ratio of Hydrophobic Residues. Front Microbiol 2021; 12:773076. [PMID: 34733268 PMCID: PMC8558516 DOI: 10.3389/fmicb.2021.773076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 12/02/2022] Open
Abstract
With the increasing number of drug-resistant bacteria, there is an urgent need for new antimicrobial agents, and antimicrobial peptides (AMPs), which exist in the human non-specific immune system, are one of the most promising candidates. It is an effective optimization strategy to modify antimicrobial peptides (AMPs) according to the distribution of amino acids and hydrophobic characteristics. The addition of bacterial pheromones to the N short peptide can increase the ability to recognize bacteria. In this study, we designed and synthesized AMP1–6 by amino acid substitution of mBjAMP1. Additionally, P-6, S-6, and L-6 were designed and synthesized by adding bacterial pheromones based on 1–6. Functional tests showed that the four AMPs had the ability to kill Gram-negative Vibrio anguillarum, Pseudomonas mendocina, and Vibrio parahaemolyticus, and Gram-positive Micrococcus luteus and Listeria monocytogenes. Additionally, all four AMPs induced permeabilization and depolarization of bacterial cell membranes and increased intracellular reactive oxygen species (ROS) levels. Importantly, they had little or no mammalian cytotoxicity. At the same time, 1–6 and L-6 protected the stability of intestinal flora in Sebastes schlegelii and increased the relative abundance of Lactobacillaceae. In summary, our results indicate that the designed AMPs have broad application prospects as a new type of polypeptide antimicrobial agent.
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Affiliation(s)
- Rong Tan
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Meiru Wang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Huiqin Xu
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Lu Qin
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Jun Wang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Pengfei Cui
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Shaoguo Ru
- College of Marine Life Science, Ocean University of China, Qingdao, China
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9
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Chakraborty G, Bardhan S, Saha SK. Unfolding of Tryptophanoctyl Ester and Elastic Deformation of Host Micelles via RR' 3 N + ⋅⋅⋅π Interaction: Conceivable Relevance to Wrapping Process of Receptor Mediated Endocytosis. Chemphyschem 2021; 22:2535-2549. [PMID: 34561950 DOI: 10.1002/cphc.202100582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 11/11/2022]
Abstract
The interfacial properties of the mixed amphiphiles are modified by a stronger cation-π interaction between the quaternary ammonium head group of CTAB and the π-face of TROE, compared to the tyrosine analogue (TYOE). This eventually triggers a morphology transition through elastic deformation of the spherical micelles of CTAB to cylindrical/wormlike micelles. The unfolding of TROE and the molecular interactions in the nanoenvironment have been recognized by NMR spectroscopy and the physical characteristics of the entangled wormlike micelles are investigated by high resolution transmission electron microscopy (HRTEM), whereas the complex fluidic feature is examined by dynamic rheological measurements. Morphology tuning of the soft nanoaggregates of zwitterionic dodecylphosphocholine by the tryptophan analogue via choline-π interaction has unique biological consequences and we consider the significance of such interactions in facilitating endocytosis of a virion/nano particle(NP) in terms of a quantitative model. The implication in future research on drug development strategies is discussed.
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Affiliation(s)
- Gulmi Chakraborty
- Department of Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Soumik Bardhan
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Swapan K Saha
- Department of Chemistry, University of North Bengal, Darjeeling, 734 013, India
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10
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Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins. CRYSTALS 2021. [DOI: 10.3390/cryst11091032] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.
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11
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Almeida CV, de Oliveira CFR, Dos Santos EL, Dos Santos HF, Júnior EC, Marchetto R, da Cruz LA, Ferreira AMT, Gomes VM, Taveira GB, Costa BO, Franco OL, Cardoso MH, Macedo MLR. Differential interactions of the antimicrobial peptide, RQ18, with phospholipids and cholesterol modulate its selectivity for microorganism membranes. Biochim Biophys Acta Gen Subj 2021; 1865:129937. [PMID: 34052310 DOI: 10.1016/j.bbagen.2021.129937] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Antimicrobial peptides (AMPs) are molecules with potential application for the treatment of microorganism infections. We, herein, describe the structure, activity, and mechanism of action of RQ18, an α-helical AMP that displays antimicrobial activity against Gram-positive and Gram-negative bacteria, and yeasts from the Candida genus. METHODS A physicochemical-guided design assisted by computer tools was used to obtain our lead peptide candidate, named RQ18. This peptide was assayed against Gram-positive and Gram-negative bacteria, yeasts, and mammalian cells to determine its selectivity index. The secondary structure and the mechanism of action of RQ18 were investigated using circular dichroism, large unilamellar vesicles, and molecular dynamic simulations. RESULTS RQ18 was not cytotoxic to human lung fibroblasts, peripheral blood mononuclear cells, red blood cells, or Vero cells at MIC values, exhibiting a high selectivity index. Circular dichroism analysis and molecular dynamic simulations revealed that RQ18 presents varying structural profiles in aqueous solution, TFE/water mixtures, SDS micelles, and lipid bilayers. The peptide was virtually unable to release carboxyfluorescein from large unilamellar vesicles composed of POPC/cholesterol, model that mimics the eukaryotic membrane, indicating that vesicles' net charges and the presence of cholesterol may be related with RQ18 selectivity for bacterial and fungal cell surfaces. CONCLUSIONS RQ18 was characterized as a membrane-active peptide with dual antibacterial and antifungal activities, without compromising mammalian cells viability, thus reinforcing its therapeutic application. GENERAL SIGNIFICANCE These results provide further insight into the complex process of AMPs interaction with biological membranes, in special with systems that mimic prokaryotic and eukaryotic cell surfaces.
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Affiliation(s)
- Claudiane V Almeida
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Caio F R de Oliveira
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil; Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil; Oncolytic Anticancer Drugs, Dourados, Mato Grosso do Sul, Brazil
| | - Edson L Dos Santos
- Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Helder F Dos Santos
- Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Edson C Júnior
- Instituto de Química, Departamento de Bioquímica e Química Tecnológica, Universidade Estadual Paulista Júlio de Mesquita Filho, Araraquara, São Paulo, Brazil
| | - Reinaldo Marchetto
- Instituto de Química, Departamento de Bioquímica e Química Tecnológica, Universidade Estadual Paulista Júlio de Mesquita Filho, Araraquara, São Paulo, Brazil
| | - Leticia A da Cruz
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Alda Maria T Ferreira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Valdirene M Gomes
- Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Gabriel B Taveira
- Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Bruna O Costa
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Marlon H Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Maria Lígia R Macedo
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
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12
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Ang QA, Arfan G, Ong CYF, Ng FM, Ong EHQ, Chia CSB. Designing a leucine-rich antibacterial nonapeptide with potent activity against mupirocin-resistant MRSA via a structure-activity relationship study. Chem Biol Drug Des 2021; 97:1185-1193. [PMID: 33754480 DOI: 10.1111/cbdd.13840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 02/19/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is the main aetiological agent responsible for the majority of human skin infections. Of particular concern is the methicillin-resistant variety, commonly known as MRSA. The extensive use of the first-line topical antibiotic of choice, mupirocin, has inevitably resulted in the emergence of resistant strains, signalling an urgent need for the development of new antibacterials with new mechanisms of action. In this work, we describe how we designed a novel cationic nonapeptide, containing only leucine and two lysine residues, with potent anti-MRSA activity and a rapid bactericidal mode of action. Coupled to a favourable safety profile towards human skin fibroblasts, we believe nonapeptide 11 has high potential for further development as a mupirocin replacement candidate to treat skin infections caused by MRSA.
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Affiliation(s)
- Qi An Ang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Giovinna Arfan
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chu Yang Fann Ong
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Fui Mee Ng
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Esther H Q Ong
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Cheng San Brian Chia
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore
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13
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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14
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Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. SCIENCE ADVANCES 2020; 6:6/39/eabb7620. [PMID: 32978166 PMCID: PMC7518861 DOI: 10.1126/sciadv.abb7620] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/12/2020] [Indexed: 05/11/2023]
Abstract
Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.
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Affiliation(s)
- Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yichong Lao
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yanee Wutthinitikornkit
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Aodong Zou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Lingyun Yang
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai 201210, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China.
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
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15
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Khan HM, Souza PCT, Thallmair S, Barnoud J, de Vries AH, Marrink SJ, Reuter N. Capturing Choline-Aromatics Cation-π Interactions in the MARTINI Force Field. J Chem Theory Comput 2020; 16:2550-2560. [PMID: 32096995 PMCID: PMC7175457 DOI: 10.1021/acs.jctc.9b01194] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Cation−π
interactions play an important
role in biomolecular recognition, including interactions between membrane
phosphatidylcholine lipids and aromatic amino acids of peripheral
proteins. While molecular mechanics coarse grain (CG) force fields
are particularly well suited to simulate membrane proteins in general,
they are not parameterized to explicitly reproduce cation−π
interactions. We here propose a modification of the polarizable MARTINI
coarse grain (CG) model enabling it to model membrane binding events
of peripheral proteins whose aromatic amino acid interactions with
choline headgroups are crucial for their membrane binding. For this
purpose, we first collected and curated a dataset of eight peripheral
proteins from different families. We find that the MARTINI CG model
expectedly underestimates aromatics–choline interactions and
is unable to reproduce membrane binding of the peripheral proteins
in our dataset. Adjustments of the relevant interactions in the polarizable
MARTINI force field yield significant improvements in the observed
binding events. The orientation of each membrane-bound protein is
comparable to reference data from all-atom simulations and experimental
binding data. We also use negative controls to ensure that choline–aromatics
interactions are not overestimated. We finally check that membrane
properties, transmembrane proteins, and membrane translocation potential
of mean force (PMF) of aromatic amino acid side-chain analogues are
not affected by the new parameter set. This new version “MARTINI
2.3P” is a significant improvement over its predecessors and
is suitable for modeling membrane proteins including peripheral membrane
binding of peptides and proteins.
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Affiliation(s)
- Hanif M Khan
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway.,Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway
| | - Paulo C T Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Jonathan Barnoud
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, Netherlands
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, N-5020 Bergen, Norway.,Department of Chemistry, University of Bergen, N-5020 Bergen, Norway
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16
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Lin FY, MacKerell AD. Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. J Comput Chem 2020; 41:439-448. [PMID: 31518010 PMCID: PMC7322827 DOI: 10.1002/jcc.26067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/15/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Fang-Yu Lin
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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17
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Wood I, Fabian L, Moglioni A, Cabeça LF, de Paula E, Pickholz M. Combining nuclear magnetic resonance with molecular dynamics simulations to address sumatriptan interaction with model membranes. Chem Phys Lipids 2019; 225:104792. [DOI: 10.1016/j.chemphyslip.2019.104792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
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18
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Functionalized olympicene (C19H12) as anode material for Li-ion batteries: a DFT approach. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02500-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Mbaye MN, Hou Q, Basu S, Teheux F, Pucci F, Rooman M. A comprehensive computational study of amino acid interactions in membrane proteins. Sci Rep 2019; 9:12043. [PMID: 31427701 PMCID: PMC6700154 DOI: 10.1038/s41598-019-48541-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/07/2019] [Indexed: 01/26/2023] Open
Abstract
Transmembrane proteins play a fundamental role in a wide series of biological processes but, despite their importance, they are less studied than globular proteins, essentially because their embedding in lipid membranes hampers their experimental characterization. In this paper, we improved our understanding of their structural stability through the development of new knowledge-based energy functions describing amino acid pair interactions that prevail in the transmembrane and extramembrane regions of membrane proteins. The comparison of these potentials and those derived from globular proteins yields an objective view of the relative strength of amino acid interactions in the different protein environments, and their role in protein stabilization. Separate potentials were also derived from α-helical and β-barrel transmembrane regions to investigate possible dissimilarities. We found that, in extramembrane regions, hydrophobic residues are less frequent but interactions between aromatic and aliphatic amino acids as well as aromatic-sulfur interactions contribute more to stability. In transmembrane regions, polar residues are less abundant but interactions between residues of equal or opposite charges or non-charged polar residues as well as anion-π interactions appear stronger. This shows indirectly the preference of the water and lipid molecules to interact with polar and hydrophobic residues, respectively. We applied these new energy functions to predict whether a residue is located in the trans- or extramembrane region, and obtained an AUC score of 83% in cross validation, which demonstrates their accuracy. As their application is, moreover, extremely fast, they are optimal instruments for membrane protein design and large-scale investigations of membrane protein stability.
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Affiliation(s)
- Mame Ndew Mbaye
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Mathematics and Informatics, Cheikh Anta Diop University, Dakar-Fann, Senegal
| | - Qingzhen Hou
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sankar Basu
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabian Teheux
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,John von Neumann Institute for Computing, Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
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20
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Waheed Q, Khan HM, He T, Roberts M, Gershenson A, Reuter N. Interfacial Aromatics Mediating Cation-π Interactions with Choline-Containing Lipids Can Contribute as Much to Peripheral Protein Affinity for Membranes as Aromatics Inserted below the Phosphates. J Phys Chem Lett 2019; 10:3972-3977. [PMID: 31246477 DOI: 10.1021/acs.jpclett.9b01639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Membrane-binding interfaces of peripheral proteins are restricted to a small part of their exposed surface, so the ability to engage in strong selective interactions with membrane lipids at various depths in the interface, both below and above the phosphates, is an advantage. Driven by their hydrophobicity, aromatic amino acids preferentially partition into membrane interfaces, often below the phosphates, yet enthalpically favorable interactions with the lipid headgroups, above the phosphate plane, are likely to further stabilize high interfacial positions. Using free-energy perturbation, we calculate the energetic cost of alanine substitution for 11 interfacial aromatic amino acids from 3 peripheral proteins. We show that the involvement in cation-π interactions with the headgroups (i) increases the ΔΔGtransfer as compared with insertion at the same depth without cation-π stabilization and (ii) can contribute at least as much as deeper insertion below the phosphates, highlighting the multiple roles of aromatics in peripheral membrane protein affinity.
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Affiliation(s)
- Qaiser Waheed
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Hanif M Khan
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Tao He
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Mary Roberts
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
- Molecular and Cellular Biology Graduate Program , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
- Department of Chemistry , University of Bergen , N-5020 Bergen , Norway
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21
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Kanti De S, Chakraborty A. Interaction of monomeric and self-assembled aromatic amino acids with model membranes: self-reproduction phenomena. Chem Commun (Camb) 2019; 55:15109-15112. [DOI: 10.1039/c9cc08495a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The spontaneous formation of amyloid structures of proteins is responsible for several major human neurodegenerative diseases.
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Affiliation(s)
- Soumya Kanti De
- Discipline of Chemistry
- Indian Institute of Technology
- Indore 453552
- India
| | - Anjan Chakraborty
- Discipline of Chemistry
- Indian Institute of Technology
- Indore 453552
- India
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22
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Khan HM, MacKerell AD, Reuter N. Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field. J Chem Theory Comput 2018; 15:7-12. [PMID: 30562013 DOI: 10.1021/acs.jctc.8b00839] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cation-π interactions between tryptophan and choline or trimethylated lysines are vital for many biological processes. The performance of the additive CHARMM36 force field against target quantum mechanical data is shown to reproduce QM equilibrium geometries but required modified Lennard-Jones potentials to accurately reproduce the QM interaction energies. The modified parameter set allows accurate modeling, including free energies, of cation-π indole-choline and indole-trimethylated lysines interactions relevant for protein-ligand, protein-membrane, and protein-protein interfaces.
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Affiliation(s)
- Hanif M Khan
- Department of Biological Sciences , University of Bergen , N-5020 Bergen , Norway.,Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics , University of Bergen , N-5020 Bergen , Norway.,Department of Chemistry , University of Bergen , N-5020 Bergen , Norway
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23
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Arfan G, Ong CYF, Ng SMS, Lau QY, Ng FM, Ong EHQ, Hill J, Chia CSB. Designing an ultra-short antibacterial peptide with potent activity against Mupirocin-resistant MRSA. Chem Biol Drug Des 2018; 93:4-11. [DOI: 10.1111/cbdd.13377] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/17/2018] [Accepted: 07/22/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Giovinna Arfan
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Chu Yang Fann Ong
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Siew Mei Samantha Ng
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Qiu Ying Lau
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Esther Hong Qian Ong
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Cheng San Brian Chia
- Experimental Therapeutics Centre; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
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24
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Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition, and Capture Properties. J Phys Chem B 2018; 122:7555-7568. [DOI: 10.1021/acs.jpcb.8b04103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
| | | | - Emmanouela Fotopoulou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
| | | | | | - Woo Taik Lim
- Department of Applied Chemistry, Andong National University, Andong 36729, Republic of Korea
| | - Sang June Choi
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
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25
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Wang Y, Cui P, Zhang Y, Yang Q, Zhang S. Augmentation of the antibacterial activities of Pt5-derived antimicrobial peptides (AMPs) by amino acid substitutions: Design of novel AMPs against MDR bacteria. FISH & SHELLFISH IMMUNOLOGY 2018; 77:100-111. [PMID: 29567140 DOI: 10.1016/j.fsi.2018.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/06/2018] [Accepted: 03/17/2018] [Indexed: 06/08/2023]
Abstract
The ever-growing concerns on multi-drug resistant (MDR) bacteria lead to urgent demands for novel antibiotics including antimicrobial peptides (AMPs). Pt5, a peptide consisting of the C-terminal 55 residues of zebrafish phosvitin, has been shown to function as an antibacterial agent. Here we used Pt5 as a template to design new AMPs by shortening the sequence and substituting with tryptophan (W) and lysine (K) at selected positions. Among the resultant Pt5-derived peptides, Pt5-1c showed the strongest antimicrobial activity against both Gram-negative and Gram-positive bacteria, including MDR bacteia, with the minimum inhibitory concentrations (MICs) ranging from 1.2 μM to 4.8 μM. Electron microscopic examination showed that Pt5-1c was able to kill the bacteria directly. ELISA revealed that Pt5-1c possessed high affinity to lipopolysaccharide (LPS), lipoteichoic acid (LTA) and peptidoglycan (PGN). Importantly, Pt5-1c was able to disrupt the bacterial membrane by a combined action of membrane depolarization and permeabilization, with little cytotoxicity to mammalian cells. Taken together, these findings suggest that Pt5-1c has considerable potential for future development as novel peptide antibiotics against MDR bacteria.
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Affiliation(s)
- Yashuo Wang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Qingdao 266003, China; Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Pengfei Cui
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Qingdao 266003, China; Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Yubo Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Qingdao 266003, China; Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Qingyun Yang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Qingdao 266003, China; Department of Marine Biology, Ocean University of China, Qingdao 266003, China
| | - Shicui Zhang
- Laboratory for Evolution & Development, Institute of Evolution & Marine Biodiversity, Qingdao 266003, China; Department of Marine Biology, Ocean University of China, Qingdao 266003, China.
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26
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García-Pindado J, Willemse T, Goss R, Maes BUW, Giralt E, Ballet S, Teixidó M. Bromotryptophans and their incorporation in cyclic and bicyclic privileged peptides. Biopolymers 2018. [DOI: 10.1002/bip.23112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Júlia García-Pindado
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Program, Barcelona Institute of Science and Technology (BIST); Barcelona 08028 Spain
| | - Tom Willemse
- Research Group of Organic, Department of Chemistry; Vrije Universiteit Brussel; Brussels 1050 Belgium
- Research Group of Organic, Department of Bioengineering Sciences; Vrije Universiteit Brussel; Brussels 1050 Belgium
- Organic Synthesis; University of Antwerp; Antwerp B-2020 Belgium
| | - Rebecca Goss
- School of Chemistry and BSRC; University of St Andrews; St Andrews KY16 9ST United Kingdom
| | - Bert U. W. Maes
- Organic Synthesis; University of Antwerp; Antwerp B-2020 Belgium
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Program, Barcelona Institute of Science and Technology (BIST); Barcelona 08028 Spain
- Department of Inorganic and Organic Chemistry; University of Barcelona; Barcelona 08028 Spain
| | - Steven Ballet
- Research Group of Organic, Department of Chemistry; Vrije Universiteit Brussel; Brussels 1050 Belgium
- Research Group of Organic, Department of Bioengineering Sciences; Vrije Universiteit Brussel; Brussels 1050 Belgium
| | - Meritxell Teixidó
- Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Program, Barcelona Institute of Science and Technology (BIST); Barcelona 08028 Spain
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27
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Ng SMS, Yap JM, Lau QY, Ng FM, Ong EHQ, Barkham T, Teo JWP, Alfatah M, Kong KW, Hoon S, Arumugam P, Hill J, Brian Chia CS. Structure-activity relationship studies of ultra-short peptides with potent activities against fluconazole-resistant Candida albicans. Eur J Med Chem 2018; 150:479-490. [PMID: 29549835 DOI: 10.1016/j.ejmech.2018.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 11/30/2022]
Abstract
Vulvovaginal candidiasis (VVC) is a genital fungal infection afflicting approximately 75% of women globally and is primarily caused by the yeast Candida albicans. The extensive use of fluconazole, the first-line antifungal drug of choice, has led to the emergence of fluconazole-resistant C. albicans, creating a global clinical concern. This, coupled to the lack of new antifungal drugs entering the market over the past decade, has made it imperative for the introduction of new antifungal drug classes. Peptides with antifungal properties are deemed potential drug candidates due to their rapid membrane-disrupting mechanism of action. By specifically targeting and rapidly disrupting fungal membranes, they reduce the chances of resistance development and treatment duration. In a previous screening campaign involving an antimicrobial peptide library, we identified an octapeptide (IKIKIKIK-NH2) with potent activity against C. albicans. Herein, we report a structure-activity relationship study on this peptide with the aim of designing a more potent peptide for further development. The lead peptide was then tested against a panel of fluconazole-resistant C. albicans, subjected to a fungicidal/static determination assay, a human dermal fibroblast viability assay and a homozygous profiling assay to gain insights into its mechanism of action and potential for further development as a topical antifungal agent.
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Affiliation(s)
- Siew Mei Samantha Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Jia Mao Yap
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Esther Hong Qian Ong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Jeanette Woon Pei Teo
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Mohammad Alfatah
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Kiat Whye Kong
- Molecular Engineering Lab, 61 Biopolis Drive, #03-12, Proteos, 138673, Singapore
| | - Shawn Hoon
- Molecular Engineering Lab, 61 Biopolis Drive, #03-12, Proteos, 138673, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore
| | - Cheng San Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore, 138669, Singapore.
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Kozic M, Fox SJ, Thomas JM, Verma CS, Rigden DJ. Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. Proteins 2018; 86:548-565. [DOI: 10.1002/prot.25473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Mara Kozic
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Stephen J. Fox
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Jens M. Thomas
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
| | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
- Department of Biological Sciences; National University of Singapore; Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
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Situ AJ, Kang SM, Frey BB, An W, Kim C, Ulmer TS. Membrane Anchoring of α-Helical Proteins: Role of Tryptophan. J Phys Chem B 2018; 122:1185-1194. [PMID: 29323921 PMCID: PMC11025564 DOI: 10.1021/acs.jpcb.7b11227] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The function of membrane proteins relies on a defined orientation of protein relative to lipid. In apparent correlation to protein anchoring, tryptophan residues are enriched in the lipid headgroup region. To characterize the thermodynamic and structural basis of this relationship in α-helical membrane proteins, we examined the role of three conserved tryptophans in the folding of the heterodimeric integrin αIIbβ3 transmembrane (TM) complex in phospholipid bicelles and mammalian membranes. In the homogenous lipid environment of bicelles, tryptophan was replaceable by residues of distinct polarities. The appropriate polarity was guided by the electrostatic potential of the tryptophan surrounding, suggesting that tryptophan can complement diverse environments by adjusting the orientation of its anisotropic side chain to achieve site-specific anchoring. As a sole membrane anchor, tryptophan made a contribution of 0.4 kcal/mol to TM complex stability in bicelles. In membranes, it proved more difficult to replace tryptophan even by tyrosine, indicating a superior capacity to interact with heterogeneous lipids of biological membranes. Interestingly, at intracellular TM helix ends, where integrin activation is initiated, sequence motifs that interact with lipids via opposing polarity patterns were found to restrict TM helix orientations beyond tryptophan anchoring. In contrast to bicelles, phenylalanine became the least accepted substitute in membranes, demonstrating an increased role of the hydrophobic effect. Altogether, our study implicates a wide amphiphilic range of tryptophan, membrane complexity, and the hydrophobic effect to be important factors in tryptophan membrane anchoring.
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Affiliation(s)
- Alan J Situ
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , 1501 San Pablo Street, Los Angeles, California 90033, United States
| | - So-Min Kang
- Department of Life Sciences, Korea University , 145 Anam-Ro, Seongbuk-Gu, Seoul 136-701, South Korea
| | - Benjamin B Frey
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , 1501 San Pablo Street, Los Angeles, California 90033, United States
| | - Woojin An
- Department of Biochemistry & Molecular Medicine and Norris Comprehensive Cancer Center, University of Southern California , Los Angeles, California 90033, United States
| | - Chungho Kim
- Department of Life Sciences, Korea University , 145 Anam-Ro, Seongbuk-Gu, Seoul 136-701, South Korea
| | - Tobias S Ulmer
- Department of Biochemistry & Molecular Medicine and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , 1501 San Pablo Street, Los Angeles, California 90033, United States
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30
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Cytotoxicity and Antibacterial Effect of Trp-Substituted CM11 Cationic Peptide Against Drug-Resistant Isolates of Brucella melitensis Alone and in Combination with Recommended Antibiotics. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-017-9658-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Ng SMS, Yap YYA, Cheong JWD, Ng FM, Lau QY, Barkham T, Teo JWP, Hill J, Chia CSB. Antifungal peptides: a potential new class of antifungals for treating vulvovaginal candidiasis caused by fluconazole-resistant Candida albicans. J Pept Sci 2017; 23:215-221. [PMID: 28105725 DOI: 10.1002/psc.2970] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 11/06/2022]
Abstract
Vulvovaginal candidiasis/candidosis is a common fungal infection afflicting approximately 75% of women globally caused primarily by the yeast Candida albicans. Fluconazole is widely regarded as the antifungal drug of choice since its introduction in 1990 due to its high oral bioavailability, convenient dosing regimen and favourable safety profile. However, its widespread use has led to the emergence of fluconazole-resistant C. albicans, posing a universal clinical concern. Coupled to the dearth of new antifungal drugs entering the market, it is imperative to introduce new drug classes to counter this threat. Antimicrobial peptides (AMPs) are potential candidates due to their membrane-disrupting mechanism of action. By specifically targeting fungal membranes and being rapidly fungicidal, they can reduce the chances of resistance development and treatment duration. Towards this goal, we conducted a head-to-head comparison of 61 short linear AMPs from the literature to identify the peptide with the most potent activity against fluconazole-resistant C. albicans. The 11-residue peptide, P11-6, was identified and assayed against a panel of clinical C. albicans isolates followed by fungicidal/static determination and a time-kill assay to gauge its potential for further drug development. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Siew Mei Samantha Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Yi Yong Alvin Yap
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Jin Wei Darryl Cheong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Jeanette Woon Pei Teo
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, 119074, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Cheng San Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
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32
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Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RWA, Reuter N. Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me) 4+ Interactions. J Chem Theory Comput 2016; 12:5585-5595. [PMID: 27682345 PMCID: PMC5148683 DOI: 10.1021/acs.jctc.6b00654] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.
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Affiliation(s)
- Hanif M Khan
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | | | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Remco W A Havenith
- Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University , 9000 Ghent, Belgium
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
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33
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Cornelio K, Espiritu RA, Todokoro Y, Hanashima S, Kinoshita M, Matsumori N, Murata M, Nishimura S, Kakeya H, Yoshida M, Matsunaga S. Sterol-dependent membrane association of the marine sponge-derived bicyclic peptide Theonellamide A as examined by 1H NMR. Bioorg Med Chem 2016; 24:5235-5242. [DOI: 10.1016/j.bmc.2016.08.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 11/29/2022]
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34
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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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35
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Ma J, Domicevica L, Schnell JR, Biggin PC. Position and orientational preferences of drug-like compounds in lipid membranes: a computational and NMR approach. Phys Chem Chem Phys 2016; 17:19766-76. [PMID: 26153345 DOI: 10.1039/c5cp03218k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Permeation of drugs across lipid bilayers is a key factor in dictating how effective they will be. In vivo, the issue is compounded by the presence of drug-exporter proteins such as P-glycoprotein. However, despite intense effort, exactly what controls permeation and susceptibility to export is still poorly understood. In this work we examine two well-studied drugs for which interaction with P-glycoprotein has been studied before: amitriptyline, a known substrate and clozapine, which is not a substrate. Extensive MD simulations, including potential of mean force (PMF) profiles of the compounds in all possible protonation states, reveal that the preferred location of the compounds in different bilayers in different protonation states is remarkably similar. For both molecules in charged states, there is a substantial barrier to crossing the bilayer. Clozapine however, shows an energetic barrier to movement across the bilayer even in a protonation state that results in an uncharged molecule. For amitriptyline there is only a very small barrier of approximately 1.3 kcal mol(-1). Further analysis revealed that the conformational and orientational behavior of the two compounds was also similar, with the sidechain interacting with the lipid headgroups. This effect was much stronger if the sidechain was charged (protonated). These interactions with lipid bilayers were confirmed by NMR ROESY experiments. The results are discussed in terms of their potential interactions with export proteins like P-glycoprotein.
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Affiliation(s)
- Jerome Ma
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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36
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Antonenko YN, Gluhov GS, Firsov AM, Pogozheva ID, Kovalchuk SI, Pechnikova EV, Kotova EA, Sokolova OS. Gramicidin A disassembles large conductive clusters of its lysine-substituted derivatives in lipid membranes. Phys Chem Chem Phys 2016; 17:17461-70. [PMID: 26077982 DOI: 10.1039/c5cp02047f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-terminally substituted lysine derivatives of gramicidin A (gA), [Lys1]gA and [Lys3]gA, but not glutamate- or aspartate-substituted peptides have been previously shown to cause the leakage of carboxyfluorescein from liposomes. Here, the leakage induction was also observed for [Arg1]gA and [Arg3]gA, while [His1]gA and [His3]gA were inactive at neutral pH. The Lys3-containing analogue with all tryptophans replaced by isoleucines did not induce liposome leakage, similar to gA. This suggests that the presence of both tryptophans and N-terminal cationic residues is critical for pore formation. Remarkably, the addition of gA blocked the leakage induced by [Lys3]gA. By examining with fluorescence correlation spectroscopy the peptide-induced leakage of fluorescent markers from liposomes, we estimated the diameter of pores responsible for the leakage to be about 1.6 nm. Transmission electron cryo-microscopy imaging of liposomes with [Lys3]gA showed that the liposomal membranes contained high electron density particles with a size of about 40 Å, suggesting the formation of peptide clusters. No such clusterization was observed in liposomes incorporating gA or a mixture of gA with [Lys3]gA. Three-dimensional reconstruction of the clusters was compatible with their pentameric arrangement. Based on experimental data and computational modeling, we suggest that the large pore formed by [Lys3]gA represents a barrel-stave oligomeric cluster formed by antiparallel double-stranded helical dimers (DH). In a tentative model, the pentamer of dimers may be stabilized by aromatic Trp-Trp and cation-π Trp-Lys interactions between the neighboring DHs. The inhibiting effect of gA on the [Lys3]gA-induced leakage can be attributed to breaking of cation-π interactions, which prevents peptide clusterization and pore formation.
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Affiliation(s)
- Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.
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37
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Gao S, Shi G, Fang H. Impact of cation-π interactions on the cell voltage of carbon nanotube-based Li batteries. NANOSCALE 2016; 8:1451-1455. [PMID: 26676257 DOI: 10.1039/c5nr06456b] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbon nanotube (CNT)-based Li batteries have attracted wide attention because of their high capacity, high cyclability and high energy density and are believed to be one of the most promising electrochemical energy storage systems. In CNT-based Li batteries, the main interaction between the Li(+) ions and the CNT is the cation-π interaction. However, up to now, it is still not clear how this interaction affects the storage characteristics of CNT-based Li batteries. Here, using density functional theory (DFT) calculations, we report a highly favorable impact of cation-π interactions on the cell voltage of CNT-based Li batteries. Considering both Li(+)-π interaction and Li-π interaction, we show that cell voltage enhances with the increase of the CNT diameter. In addition, when the Li(+) ion adsorbs on the external wall, the cell voltage is larger than that when it adsorbs on the internal wall. This suggests that CNTs with a large diameter and a low array density are more advantageous to enhance storage performance of CNT-based Li batteries. Compared with Li(+) ions on the (4,4) CNT internal wall, the cell voltage of Li(+) on the (10,10) CNT external wall is 0.55 V higher, which indicates an improvement of about 38%. These results will be helpful for the design of more efficient CNT-based Li batteries.
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Affiliation(s)
- Shaohua Gao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China.
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China.
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38
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Shagaghi N, Palombo EA, Clayton AHA, Bhave M. Archetypal tryptophan-rich antimicrobial peptides: properties and applications. World J Microbiol Biotechnol 2016; 32:31. [PMID: 26748808 DOI: 10.1007/s11274-015-1986-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022]
Abstract
Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.
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Affiliation(s)
- Nadin Shagaghi
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Enzo A Palombo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Andrew H A Clayton
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Mrinal Bhave
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia.
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39
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Baker CM, Grant GH. Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine. J Chem Theory Comput 2015; 3:530-48. [PMID: 26637033 DOI: 10.1021/ct600218f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aromatic groups are now acknowledged to play an important role in many systems of interest. However, existing molecular mechanics methods provide a poor representation of these groups. In a previous paper, we have shown that the molecular mechanics treatment of benzene can be improved by the incorporation of an explicit representation of the aromatic π electrons. Here, we develop this concept further, developing charge-separation models for toluene, phenol, and pyridine. Monte Carlo simulations are used to parametrize the models, via the reproduction of experimental thermodynamic data, and our models are shown to outperform an existing atom-centered model. The models are then used to make predictions about the structures of the liquids at the molecular level and are tested further through their application to the modeling of gas-phase dimers and cation-π interactions.
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Affiliation(s)
- Christopher M Baker
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom, and Unilever Centre for Molecular Informatics, The University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Guy H Grant
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom, and Unilever Centre for Molecular Informatics, The University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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40
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Yahyaa M, Matsuba Y, Brandt W, Doron-Faigenboim A, Bar E, McClain A, Davidovich-Rikanati R, Lewinsohn E, Pichersky E, Ibdah M. Identification, Functional Characterization, and Evolution of Terpene Synthases from a Basal Dicot. PLANT PHYSIOLOGY 2015; 169:1683-97. [PMID: 26157114 PMCID: PMC4634067 DOI: 10.1104/pp.15.00930] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 05/06/2023]
Abstract
Bay laurel (Laurus nobilis) is an agriculturally and economically important dioecious tree in the basal dicot family Lauraceae used in food and drugs and in the cosmetics industry. Bay leaves, with their abundant monoterpenes and sesquiterpenes, are used to impart flavor and aroma to food, and have also drawn attention in recent years because of their potential pharmaceutical applications. To identify terpene synthases (TPSs) involved in the production of these volatile terpenes, we performed RNA sequencing to profile the transcriptome of L. nobilis leaves. Bioinformatic analysis led to the identification of eight TPS complementary DNAs. We characterized the enzymes encoded by three of these complementary DNAs: a monoterpene synthase that belongs to the TPS-b clade catalyzes the formation of mostly 1,8-cineole; a sesquiterpene synthase belonging to the TPS-a clade catalyzes the formation of mainly cadinenes; and a diterpene synthase of the TPS-e/f clade catalyzes the formation of geranyllinalool. Comparison of the sequences of these three TPSs indicated that the TPS-a and TPS-b clades of the TPS gene family evolved early in the evolution of the angiosperm lineage, and that geranyllinalool synthase activity is the likely ancestral function in angiosperms of genes belonging to an ancient TPS-e/f subclade that diverged from the kaurene synthase gene lineages before the split of angiosperms and gymnosperms.
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Affiliation(s)
- Mosaab Yahyaa
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Yuki Matsuba
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Wolfgang Brandt
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Adi Doron-Faigenboim
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Einat Bar
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Alan McClain
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Rachel Davidovich-Rikanati
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Efraim Lewinsohn
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Eran Pichersky
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
| | - Mwafaq Ibdah
- Newe Yaar Research Center, Agriculture Research Organization, Ramat Yishay 30095, Israel (M.Y., A.D.-F., E.B., R.D.-R., E.L., M.I.);Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (Y.M., A.M., E.P.); andDepartment of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany (W.B.)
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Discovery of an ultra-short linear antibacterial tetrapeptide with anti-MRSA activity from a structure-activity relationship study. Eur J Med Chem 2015; 105:138-44. [PMID: 26489599 DOI: 10.1016/j.ejmech.2015.10.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 11/20/2022]
Abstract
The overuse and misuse of antibiotics has resulted in the emergence of drug-resistant pathogenic bacteria, including meticillin-resistant Staphylococcus aureus (MRSA), the primary pathogen responsible for human skin and soft-tissue infections. Antibacterial peptides are known to kill bacteria by rapidly disrupting their membranes and are deemed plausible alternatives to conventional antibiotics. One advantage of their membrane-targeting mode of action is that bacteria are unlikely to develop resistance as changing their cell membrane structure and morphology would likely involve extensive genetic mutations. However, major concerns in using peptides as antibacterial drugs include their instability towards plasma proteases, toxicity towards human cells due to their membrane-targeting mode of action and high manufacturing cost. These concerns can be mitigated by developing peptides as topical agents, by the judicial selection of amino acids and developing very short peptides respectively. In this preliminary report, we reveal a linear, non-hemolytic tetrapeptide with rapid bactericidal activity against MRSA developed from a structure-activity relationship study based on the antimicrobial hexapeptide WRWRWR-NH2. Our finding opens promising avenues for the development of ultra-short antibacterials to treat multidrug-resistant MRSA skin and soft tissue infections.
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Pathak AK, Bandyopadhyay T. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions. Biopolymers 2015; 105:10-20. [PMID: 26270602 DOI: 10.1002/bip.22712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/10/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023]
Abstract
Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
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Holland MC, Metternich JB, Daniliuc C, Schweizer WB, Gilmour R. Aromatic Interactions in Organocatalyst Design: Augmenting Selectivity Reversal in Iminium Ion Activation. Chemistry 2015; 21:10031-8. [PMID: 25982418 DOI: 10.1002/chem.201500270] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/12/2022]
Abstract
Substituting N-methylpyrrole for N-methyindole in secondary-amine-catalysed Friedel-Crafts reactions leads to a curious erosion of enantioselectivity. In extreme cases, this substrate dependence can lead to an inversion in the sense of enantioinduction. Indeed, these closely similar transformations require two structurally distinct catalysts to obtain comparable selectivities. Herein a focussed molecular editing study is disclosed to illuminate the structural features responsible for this disparity, and thus identify lead catalyst structures to further exploit this selectivity reversal. Key to effective catalyst re-engineering was delineating the non-covalent interactions that manifest themselves in conformation. Herein we disclose preliminary validation that intermolecular aromatic (CH-π and cation-π) interactions between the incipient iminium cation and the indole ring system is key to rationalising selectivity reversal. This is absent in the N-methylpyrrole alkylation, thus forming the basis of two competing enantio-induction pathways. A simple L-valine catalyst has been developed that significantly augments this interaction.
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Affiliation(s)
- Mareike C Holland
- Institut für Organische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster (Germany) http://www.uni-muenster.de/Chemie.oc/gilmour/,Current address: Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles 90095-1569 (USA)
| | - Jan Benedikt Metternich
- Institut für Organische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster (Germany) http://www.uni-muenster.de/Chemie.oc/gilmour/
| | - Constantin Daniliuc
- Institut für Organische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster (Germany) http://www.uni-muenster.de/Chemie.oc/gilmour/
| | - W Bernd Schweizer
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
| | - Ryan Gilmour
- Institut für Organische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster (Germany) http://www.uni-muenster.de/Chemie.oc/gilmour/. .,Excellence Cluster EXC 1003 "Cells in Motion", Westfälische Wilhelms-Universität Münster, Münster (Germany).
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Johnston AJ, Zhang YR, Busch S, Pardo LC, Imberti S, McLain SE. Amphipathic solvation of indole: implications for the role of tryptophan in membrane proteins. J Phys Chem B 2015; 119:5979-87. [PMID: 25893741 DOI: 10.1021/acs.jpcb.5b02476] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microscopic structure of the tryptophan side chain, indole, in an amphiphilic environment has been investigated using a combination of neutron diffraction measurements and simulations in solution. The results show that indole is preferentially solvated by hydrogen bonding interactions between water and alcohol -OH groups rather than the interaction being dominated by indole-methyl interactions. This has implications for understanding how tryptophan interacts with the amphipathic membrane environment to anchor proteins into membranes, where the results here suggest that the benzene ring of tryptophan interacts directly with the interfacial water at the membrane surface rather than being buried into the hydrophobic regions of the membrane bilayer.
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Affiliation(s)
| | - Yapei Rosie Zhang
- ‡Department of Biochemistry, Princeton University, Princeton, New Jersey, United States
| | - Sebastian Busch
- ⊥German Engineering Materials Science Centre (GEMS), Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH Lichtenbergstrasse 1, 85747 Garching bei München, Germany
| | - Luis Carlos Pardo
- §Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
| | - Silvia Imberti
- ∥ISIS Facility, Rutherford Appleton Laboratory, Didcot, Chilton, U.K
| | - Sylvia E McLain
- †Department of Biochemistry, University of Oxford, Oxford, U.K
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Visentin M, Unal ES, Najmi M, Fiser A, Zhao R, Goldman ID. Identification of Tyr residues that enhance folate substrate binding and constrain oscillation of the proton-coupled folate transporter (PCFT-SLC46A1). Am J Physiol Cell Physiol 2015; 308:C631-41. [PMID: 25608532 DOI: 10.1152/ajpcell.00238.2014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/20/2015] [Indexed: 12/15/2022]
Abstract
The proton-coupled folate transporter (PCFT) mediates intestinal folate absorption and transport of folates across the choroid plexus. This study focuses on the role of Tyr residues in PCFT function. The substituted Cys-accessibility method identified four Tyr residues (Y291, Y362, Y315, and Y414) that are accessible to the extracellular compartment; three of these (Y291, Y362, and Y315) are located within or near the folate binding pocket. When the Tyr residues were replaced with Cys or Ala, these mutants showed similar (up to 6-fold) increases in influx Vmax and Kt/Ki for [(3)H]methotrexate and [(3)H]pemetrexed. When the Tyr residues were replaced with Phe, these changes were moderated or absent. When Y315A PCFT was used as representative of the mutants and [(3)H]pemetrexed as the transport substrate, this substitution did not increase the efflux rate constant. Furthermore, neither influx nor efflux mediated by Y315A PCFT was transstimulated by the presence of substrate in the opposite compartment; however, substantial bidirectional transstimulation of transport was mediated by wild-type PCFT. This resulted in a threefold greater efflux rate constant for cells that express wild-type PCFT than for cells that express Y315 PCFT under exchange conditions. These data suggest that these Tyr residues, possibly through their rigid side chains, secure the carrier in a high-affinity state for its folate substrates. However, this may be achieved at the expense of constraining the carrier's mobility, thereby decreasing the rate at which the protein oscillates between its conformational states. The Vmax generated by these Tyr mutants may be so rapid that further augmentation during transstimulation may not be possible.
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Affiliation(s)
- Michele Visentin
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York
| | - Ersin Selcuk Unal
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Mitra Najmi
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York; and Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
| | - Rongbao Zhao
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - I David Goldman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York;
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Francois-Moutal L, Marcillat O, Granjon T. Structural comparison of highly similar nucleoside-diphosphate kinases: Molecular explanation of distinct membrane-binding behavior. Biochimie 2014; 105:110-8. [DOI: 10.1016/j.biochi.2014.06.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 06/30/2014] [Indexed: 02/06/2023]
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47
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Wood I, Pickholz M. Triptan partition in model membranes. J Mol Model 2014; 20:2463. [DOI: 10.1007/s00894-014-2463-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/07/2014] [Indexed: 10/24/2022]
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Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3191-202. [PMID: 25218402 DOI: 10.1016/j.bbamem.2014.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 11/22/2022]
Abstract
Neutrophil serine proteases Proteinase 3 (PR3) and human neutrophil elastase (HNE) are homologous antibiotic serine proteases of the polymorphonuclear neutrophils. Despite sharing a 56% sequence identity they have been shown to have different functions and localizations in the neutrophils. In particular, and in contrast to HNE, PR3 has been detected at the outer leaflet of the plasma membrane and its membrane expression is a risk factor in a number of chronic inflammatory diseases. Although a plethora of studies performed in various cell-based assays have been reported, the mechanism by which PR3, and possibly HNE bind to simple membrane models remains unclear. We used surface plasmon resonance (SPR) experiments to measure and compare the affinity of PR3 and HNE for large unilamellar vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). We also conducted 500-nanosecond long molecular dynamics simulations of each enzyme at the surface of a POPC bilayer to map the interactions between proteins and lipids and rationalize the difference in affinity observed in the SPR experiment. We find that PR3 binds strongly to POPC large unilamellar vesicles (Kd=9.2×10(-7)M) thanks to the insertion of three phenylalanines, one tryptophan and one leucine beyond the phosphate groups of the POPC lipids. HNE binds in a significantly weaker manner (Kd>10(-5)M) making mostly electrostatic interactions via lysines and arginines and inserting only one leucine between the hydrophobic lipid tails. Our results support the early reports that PR3, unlike HNE, is able to directly and strongly anchor directly to the neutrophil membrane.
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Chaudhuri A, Haldar S, Sun H, Koeppe RE, Chattopadhyay A. Importance of indole N-H hydrogen bonding in the organization and dynamics of gramicidin channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:419-28. [PMID: 24148157 DOI: 10.1016/j.bbamem.2013.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/25/2023]
Abstract
The linear ion channel peptide gramicidin represents an excellent model for exploring the principles underlying membrane protein structure and function, especially with respect to tryptophan residues. The tryptophan residues in gramicidin channels are crucial for the structure and function of the channel. In order to test the importance of indole hydrogen bonding for the biophysical properties of gramicidin channels, we monitored the effect of N-methylation of gramicidin tryptophans, using a combination of steady state and time-resolved fluorescence approaches along with circular dichroism spectroscopy. We show here that in the absence of the hydrogen bonding ability of tryptophans, tetramethyltryptophan gramicidin (TM-gramicidin) is unable to maintain the single stranded, head-to-head dimeric channel conformation in membranes. Our results show that TM-gramicidin displays a red-shifted fluorescence emission maximum, lower red edge excitation shift (REES), and higher fluorescence intensity and lifetime, consistent with its nonchannel conformation. This is in agreement with the measured location (average depth) of the 1-methyltryptophans in TM-gramicidin using the parallax method. These results bring out the usefulness of 1-methyltryptophan as a fluorescent tool to examine the hydrogen bonding ability of tryptophans in proteins and peptides. We conclude that changes in the hydrogen bonding ability of tryptophans, along with coupled changes in peptide backbone structure induce the loss of single stranded β(6.3) helical dimer conformation. These results agree with earlier results from size-exclusion chromatography and single-channel measurements for TM-gramicidin, and confirm the importance of indole hydrogen bonding for the conformation and function of ion channels and membrane proteins.
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Affiliation(s)
- Arunima Chaudhuri
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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