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Luo Y, Zhang Y, Xiong Z, Chen X, Sha A, Xiao W, Peng L, Zou L, Han J, Li Q. Peptides Used for Heavy Metal Remediation: A Promising Approach. Int J Mol Sci 2024; 25:6717. [PMID: 38928423 PMCID: PMC11203628 DOI: 10.3390/ijms25126717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
In recent years, heavy metal pollution has become increasingly prominent, severely damaging ecosystems and biodiversity, and posing a serious threat to human health. However, the results of current methods for heavy metal restoration are not satisfactory, so it is urgent to find a new and effective method. Peptides are the units that make up proteins, with small molecular weights and strong biological activities. They can effectively repair proteins by forming complexes, reducing heavy metal ions, activating the plant's antioxidant defense system, and promoting the growth and metabolism of microorganisms. Peptides show great potential for the remediation of heavy metal contamination due to their special structure and properties. This paper reviews the research progress in recent years on the use of peptides to remediate heavy metal pollution, describes the mechanisms and applications of remediation, and provides references for the remediation of heavy metal pollution.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jialiang Han
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610000, China; (Y.L.); (Y.Z.); (Z.X.); (X.C.); (A.S.); (W.X.); (L.P.); (L.Z.)
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610000, China; (Y.L.); (Y.Z.); (Z.X.); (X.C.); (A.S.); (W.X.); (L.P.); (L.Z.)
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2
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Koskamp JA, Ruiz Hernandez SE, de Leeuw NH, Wolthers M. Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:1220-1235. [PMID: 36524712 PMCID: PMC9811642 DOI: 10.1039/d2cp02879d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid, and dissolved ions are often studied using standard biomolecular force-fields, where the interactions between biomolecules and cations are often not parameterized explicitly. In this study, we have employed metadynamics simulations to investigate different interactions of Ca with aspartic and glutamic acid and constructed the free energy profiles of Ca2+-carboxylate association. Starting from a generally accepted, AMBER-based force field, the association was substantially over and under-estimated, depending on the choice of water model (TIP3P and SPC/fw, respectively). To rectify this discrepancy, we have replaced the default calcium parameters. Additionally, we modified the σij value in the hetero-atomic Lennard-Jones interaction by 0.5% to further improve the interaction between Ca and carboxylate, based on comparison with the experimentally determined association constant for Ca with the carboxylate group of L-aspartic acid. The corrected description retrieved the structural properties of the ion pair in agreement with the original biomolecule - Ca2+ interaction in AMBER, whilst also producing an association constant comparable to experimental observations. This refined force field was then used to investigate the interactions between amino acids, calcium and carbonate ions during biogenic and biomimetic calcium carbonate mineralisation.
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Affiliation(s)
- Janou A. Koskamp
- Department of Earth Sciences, Utrecht University3584 CB UtrechtThe Netherlands+31302535042
| | | | - Nora H. de Leeuw
- Department of Earth Sciences, Utrecht University3584 CB UtrechtThe Netherlands+31302535042,School of Chemistry, University of LeedsLeeds LS2 9JTUK
| | - Mariette Wolthers
- Department of Earth Sciences, Utrecht University3584 CB UtrechtThe Netherlands+31302535042
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3
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Lerbret A, Assifaoui A. How Accurate Is the Egg-Box Model in Describing the Binding of Calcium to Polygalacturonate? A Molecular Dynamics Simulation Study. J Phys Chem B 2022; 126:10206-10220. [PMID: 36411084 DOI: 10.1021/acs.jpcb.2c05374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We performed molecular dynamics (MD) simulations of octameric galacturonate, GalA8, chains in the presence of Ca2+ in a ratio of R = [Ca2+]/[GalA] = 0.25 in order to determine to which extent the popular "egg-box model" (EBM) is able to describe the association between Ca2+ cations and polygalacturonate (polyGalA) chains. To this aim, we slightly revised the empirical parameters for the interaction between Ca2+ and the carboxylate oxygen atoms of GalA units so as to reproduce the experimental Ca2+-GalA association constant. We also defined an ad hoc order parameter, referred to as the egg-box score (EBS), that quantifies any deviation of the local coordination geometry of calcium cations with respect to an "ideal" EBM coordination geometry. The results reveal that the local coordination geometry of Ca2+ cations bound to polyGalA chains differs from that of the EBM. Moreover, polyGalA chains exhibit significant conformational disorder, and the cross-link angles formed between polyGalA chain axes are broadly distributed. Overall, the present study suggests that the EBM fails to describe accurately the association modes between calcium and polyGalA chains at a molar ratio R of 0.25.
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Affiliation(s)
- Adrien Lerbret
- Université Bourgogne Franche-Comté, Institut Agro, UMR PAM, 1 Esplanade Erasme, 21000Dijon, France
| | - Ali Assifaoui
- Université Bourgogne Franche-Comté, Institut Agro, UMR PAM, 1 Esplanade Erasme, 21000Dijon, France
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4
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Calcium supplements and structure–activity relationship of peptide-calcium chelates: a review. Food Sci Biotechnol 2022; 31:1111-1122. [DOI: 10.1007/s10068-022-01128-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/28/2022] [Indexed: 11/04/2022] Open
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5
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Fan K, Zhang Y, Qiu Y, Zhang H. Impacts of targeting different hydration free energy references on the development of ion potentials. Phys Chem Chem Phys 2022; 24:16244-16262. [PMID: 35758314 DOI: 10.1039/d2cp01237e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration free energy (HFE) as the most important solvation parameter is often targeted in ion model development, even though the reported values differ by dozens of kcal mol-1 mainly due to the experimentally undetermined HFE of the proton ΔG°(H+). The choice of ΔG°(H+) obviously affects the hydration of single ions and the relative HFE between the ions with different (magnitude or sign) charges, and the impacts of targeted HFEs on the ion solvation and ion-ion interactions are largely unrevealed. Here we designed point charge models of K+, Mg2+, Al3+, and Cl- ions targeting a variety of HFE references and then investigated the HFE influences on the simulations of dilute and concentrated ion solutions and of the salt ion pairs in gas, liquid, and solid phases. Targeting one more property of ion-water oxygen distances (IOD) leaves the ion-water binding distance invariant, while the binding strength increases with the decreasing (more negative) HFE of ions as a result of a decrease in ΔG°(H+) for the cation and an increase in ΔG°(H+) for the anion. The increase in ΔG°(H+) leads to strengthened cation-anion interactions and thus to close ion-ion contacts, low osmotic pressures, and small activity derivatives in concentrated ion solutions as well as too stable ion pairs of the salts in different phases. The ion diffusivity and water exchange rates around the ions are simply not HFE dependent but rather more complex. Targeting both the aqueous IOD and salt crystal properties of KCl was also attempted and the comparison between different models indicates the complexity and challenge in obtaining a balanced performance between different phases using classical force fields. Our results also support that a real ΔG°(H+) value of -259.8 kcal mol-1 recommended by Hünenberger and Reif guides ion models to reproduce ion-water and ion-ion interactions reasonably at relatively low salt concentrations. Simulations of a metalloprotein show that a relatively more positive ΔG°(H+) for Mg2+ model is better for a reasonable description of the metal binding network.
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Affiliation(s)
- Kun Fan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yongguang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China.
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6
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Guan X, Tan C, Li W, Wang W, Thirumalai D. Role of water-bridged interactions in metal ion coupled protein allostery. PLoS Comput Biol 2022; 18:e1010195. [PMID: 35653400 PMCID: PMC9197054 DOI: 10.1371/journal.pcbi.1010195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 06/14/2022] [Accepted: 05/10/2022] [Indexed: 11/18/2022] Open
Abstract
Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca2+ binding and protein allostery. The bridging water molecules between Ca2+ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca2+ coupled protein allostery. Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca2+ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery. Natural proteins often utilize allostery in executing a variety of functions. Metal ions are typical cofactors to trigger the allosteric cascade. In this work, using the Ca2+ sensor protein calmodulin as the model system, we revealed crucial roles of water-bridged interactions in the metal ion coupled protein allostery. The coordination of the Ca2+ to the binding site involves an intermediate in which the water molecule bridges the Ca2+ and the liganding residue. The bridging water reduces the free energy barrier height of ligand exchange, therefore facilitating the ligand exchange and allosteric coupling by acting as a lubricant. We also showed that the response of the two symmetrically arranged EF-hand motifs of CaM domains upon Ca2+ binding is asymmetric, which is directly attributed to the differing dehydration process of the Ca2+ ions and is needed for efficient allosteric communication.
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Affiliation(s)
- Xingyue Guan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
| | - Cheng Tan
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, China
- * E-mail: (WL); (WW); (DT)
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing, China
- * E-mail: (WL); (WW); (DT)
| | - D. Thirumalai
- Department of Chemistry, University of Texas, Texas, United States of America
- * E-mail: (WL); (WW); (DT)
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7
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Schuitemaker A, Aufort J, Koziara KB, Demichelis R, Raiteri P, Gale JD. Simulating the binding of key organic functional groups to aqueous calcium carbonate species. Phys Chem Chem Phys 2021; 23:27253-27265. [PMID: 34870292 DOI: 10.1039/d1cp04226b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.
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Affiliation(s)
- Alicia Schuitemaker
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julie Aufort
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Katarzyna B Koziara
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Paolo Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julian D Gale
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
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8
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Donon J, Habka S, Very T, Charnay-Pouget F, Mons M, Aitken DJ, Brenner V, Gloaguen E. Ion Pair Supramolecular Structure Identified by ATR-FTIR Spectroscopy and Simulations in Explicit Solvent*. Chemphyschem 2021; 22:2442-2455. [PMID: 34637180 DOI: 10.1002/cphc.202100565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/17/2021] [Indexed: 11/12/2022]
Abstract
The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable force-field (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.
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Affiliation(s)
- Jeremy Donon
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Sana Habka
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Thibaut Very
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France.,IDRIS-CNRS, Campus Universitaire d'Orsay, BP 167, 91403, Orsay cedex, France
| | - Florence Charnay-Pouget
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405, Orsay cedex, France.,Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, 63000, Clermont-Ferrand, France
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - David J Aitken
- ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, UMR 8182, Bât. 420, 15 rue Georges Clémenceau, 91405, Orsay cedex, France
| | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris Saclay, CEA Saclay, Bât 522, 91191, Gif-sur-Yvette, France
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9
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Lemke T, Edte M, Gebauer D, Peter C. Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization. J Phys Chem B 2021; 125:10335-10343. [PMID: 34473925 DOI: 10.1021/acs.jpcb.1c04467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the role of polymers rich in aspartic acid (Asp) and glutamic acid (Glu) is the key to gaining precise control over mineralization processes. Despite their chemical similarity, experiments revealed a surprisingly different influence of Asp and Glu sequences. We conducted molecular dynamics simulations of Asp and Glu peptides in the presence of calcium and chloride ions to elucidate the underlying phenomena. In line with experimental differences, in our simulations, we indeed find strong differences in the way the peptides interact with ions in solution. The investigated Asp pentapeptide tends to pull a lot of ions into its vicinity, and many structures with clusters of calcium and chloride ions on the surface of the peptide can be observed. Under the same conditions, comparatively fewer ions can be found in proximity of the investigated Glu pentapeptide, and the structures are characterized by single calcium ions bound to multiple carboxylate groups. Based on our simulation data, we identified three reasons contributing to these differences, leading to a new level of understanding additive-ion interactions.
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Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Moritz Edte
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
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10
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Lin S, Hu X, Li L, Yang X, Chen S, Wu Y, Yang S. Preparation, purification and identification of iron-chelating peptides derived from tilapia (Oreochromis niloticus) skin collagen and characterization of the peptide-iron complexes. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111796] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Guvench O, Whitmore EK. Sulfation and Calcium Favor Compact Conformations of Chondroitin in Aqueous Solutions. ACS OMEGA 2021; 6:13204-13217. [PMID: 34056470 PMCID: PMC8158799 DOI: 10.1021/acsomega.1c01071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/28/2021] [Indexed: 06/01/2023]
Abstract
The effects of sulfation and calcium cations (Ca2+) on the atomic-resolution conformational properties of chondroitin carbohydrate polymers in aqueous solutions are not well studied owing to experimental challenges. Here, we compare all-atom explicit-solvent molecular dynamics simulations results for pairs of O-type (nonsulfated) and A-type (GlcNAc 4-O-sulfated) chondroitin 20-mers in 140 mM NaCl with and without Ca2+ and find that both sulfation and Ca2+ favor more compact polymer conformations. We also show that subtle differences in force-field parametrization can have dramatic effects on Ca2+ binding to chondroitin carboxylate and sulfate functional groups and thereby determine Ca2+-mediated intra- and interstrand association. In addition to providing an atomic-resolution picture of the interaction of Ca2+ with sulfated and nonsulfated chondroitin polymers, the molecular dynamics data emphasize the importance of careful force-field parametrization to balance ion-water and ion-chondroitin interactions and suggest additional parametrization efforts to tune interactions involving sulfate.
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Affiliation(s)
- Olgun Guvench
- Department
of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University
of New England, 716 Stevens
Avenue, Portland, Maine 04103, United States
- Graduate
School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, Maine 04469, United
States
| | - Elizabeth K. Whitmore
- Department
of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University
of New England, 716 Stevens
Avenue, Portland, Maine 04103, United States
- Graduate
School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, Maine 04469, United
States
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12
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Wang M, Zheng Z, Liu C, Sun H, Liu Y. Investigating the calcium binding characteristics of black bean protein hydrolysate. Food Funct 2020; 11:8724-8734. [PMID: 32945323 DOI: 10.1039/d0fo01708f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The black bean protein has been widely utilized to prepare hydrolysates with different bioactive properties. Herein, we hydrolyzed the black bean protein to prepare hydrolysate with calcium binding activity and characterized its behavior. Our results showed that ficin was superior in obtaining hydrolysate with calcium binding capacity in comparison with trypsin, alcalase and bromelain. In particular, the optimal capacity of ficin hydrolysate reached 77.54 ± 1.61 μg mg-1, where the optimal hydrolysis conditions of ficin were a temperature of 70 °C, a pH value of 6.2, an enzyme concentration of 1.61% and a time of 3 h. This might be due to high proportions of aspartic acid and glutamic acid (35.59%). Further spectral analysis evidenced the formation of hydrolysate-calcium complexes, demonstrating that the interaction between hydrolysate and calcium ions primarily occur on carboxyl oxygen atoms and amino nitrogen atoms. These findings provide a possible utilization of black bean hydrolysate to serve as a calcium supplement nutraceutical to enhance the absorption and bioavailability.
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Affiliation(s)
- Man Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Zhaojun Zheng
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Chunhuan Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Hong Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, People's Republic of China.
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13
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Maire du Poset A, Zitolo A, Cousin F, Assifaoui A, Lerbret A. Evidence for an egg-box-like structure in iron(ii)–polygalacturonate hydrogels: a combined EXAFS and molecular dynamics simulation study. Phys Chem Chem Phys 2020; 22:2963-2977. [DOI: 10.1039/c9cp04065j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The coordination of Fe(ii) with polygalacturonic acid (polyGalA) in Fe(ii)–polyGalA hydrogels exhibits an octahedral geometry that follows the “egg-box model”.
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Affiliation(s)
| | - Andrea Zitolo
- Synchrotron SOLEIL
- L’Orme des Merisiers
- BP 48 St Aubin
- 91192 Gif-sur-Yvette
- France
| | - Fabrice Cousin
- Laboratoire Léon Brillouin
- Université Paris-Saclay
- CEA-Saclay
- 91191 Gif-sur-Yvette
- France
| | - Ali Assifaoui
- Univ. Bourgogne Franche-Comté
- AgroSup Dijon
- PAM UMR A 02.102
- F-21000 Dijon
- France
| | - Adrien Lerbret
- Univ. Bourgogne Franche-Comté
- AgroSup Dijon
- PAM UMR A 02.102
- F-21000 Dijon
- France
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14
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A novel calcium-chelating peptide purified from Auxis thazard protien hydrolysate and its binding properties with calcium. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.103447] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019; 119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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16
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Zdrali E, Baer MD, Okur HI, Mundy CJ, Roke S. The Diverse Nature of Ion Speciation at the Nanoscale Hydrophobic/Water Interface. J Phys Chem B 2019; 123:2414-2423. [DOI: 10.1021/acs.jpcb.8b10207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evangelia Zdrali
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Halil I. Okur
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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17
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Purification and characterization of a novel calcium-biding decapeptide from Pacific cod (Gadus Macrocephalus) bone: Molecular properties and calcium chelating modes. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.11.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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DeMarco KR, Bekker S, Vorobyov I. Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation. J Physiol 2018; 597:679-698. [PMID: 30471114 DOI: 10.1113/jp277088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 10/15/2018] [Indexed: 12/19/2022] Open
Abstract
Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all-atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage-gated channels from the KV and NaV families, which have garnered many successes and engendered several long-standing controversies regarding the nature of their structure-function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Chemistry Department, American River College, Sacramento, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, USA.,Department of Pharmacology, School of Medicine, University of California, Davis, CA, USA
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19
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Martinek T, Duboué-Dijon E, Timr Š, Mason PE, Baxová K, Fischer HE, Schmidt B, Pluhařová E, Jungwirth P. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering. J Chem Phys 2018; 148:222813. [DOI: 10.1063/1.5006779] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tomas Martinek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
| | - Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
| | - Štěpán Timr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
| | - Katarina Baxová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
| | - Henry E. Fischer
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Burkhard Schmidt
- Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany
| | - Eva Pluhařová
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, v.v.i., Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 542/2, 160 00 Prague, Czech Republic
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Duboué-Dijon E, Delcroix P, Martinez-Seara H, Hladílková J, Coufal P, Křížek T, Jungwirth P. Binding of Divalent Cations to Insulin: Capillary Electrophoresis and Molecular Simulations. J Phys Chem B 2018; 122:5640-5648. [PMID: 29360367 DOI: 10.1021/acs.jpcb.7b12097] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present study, we characterize the binding of divalent cations to insulin in aqueous salt solutions by means of capillary electrophoresis and molecular dynamics simulations. The results show a strong pH dependence. At low pH, at which all the carboxylate groups are protonated and the protein has an overall positive charge, all the cations exhibit only weak and rather unspecific interactions with insulin. In contrast, at close to neutral pH, when all the carboxylate groups are deprotonated and negatively charged, the charge-neutralizing effect of magnesium, calcium, and zinc, in particular, on the electrophoretic mobility of insulin is significant. This is also reflected in the results of molecular dynamics simulations showing accumulation of cations at the protein surface, which becomes smaller in magnitude upon effective inclusion of electronic polarization via charge rescaling.
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Affiliation(s)
- Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , 160 00 Prague , Czech Republic
| | - Pauline Delcroix
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , 160 00 Prague , Czech Republic.,J. Heyrovský Institute of Physical Chemistry , Czech Academy of Sciences , v.v.i, Dolejškova 2155/3 , 182 23 Prague 8 , Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , 160 00 Prague , Czech Republic
| | - Jana Hladílková
- Division of Theoretical Chemistry , Lund University , POB 124, SE-22100 Lund , Sweden
| | - Pavel Coufal
- Department of Analytical Chemistry , Faculty of Science, Charles University in Prague , Albertov 2030 , 12840 Prague 2 , Czech Republic
| | - Tomáš Křížek
- Department of Analytical Chemistry , Faculty of Science, Charles University in Prague , Albertov 2030 , 12840 Prague 2 , Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 542/2 , 160 00 Prague , Czech Republic
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21
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Molecular dynamic studies of π + - π − stacked imidazolium/imidazolate ion pairs in chloroform solution. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.06.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Liu X, Lu X, Zhang Y, Zhang C, Wang R. Complexation of carboxylate on smectite surfaces. Phys Chem Chem Phys 2017; 19:18400-18406. [PMID: 28678224 DOI: 10.1039/c7cp03019c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a first principles molecular dynamics (FPMD) study of carboxylate complexation on clay surfaces. By taking acetate as a model carboxylate, we investigate its inner-sphere complexes adsorbed on clay edges (including (010) and (110) surfaces) and in interlayer space. Simulations show that acetate forms stable monodentate complexes on edge surfaces and a bidentate complex with Ca2+ in the interlayer region. The free energy calculations indicate that the complexation on edge surfaces is slightly more stable than in interlayer space. By integrating pKas and desorption free energies of Al coordinated water calculated previously (X. Liu, X. Lu, E. J. Meijer, R. Wang and H. Zhou, Geochim. Cosmochim. Acta, 2012, 81, 56-68; X. Liu, J. Cheng, M. Sprik, X. Lu and R. Wang, Geochim. Cosmochim. Acta, 2014, 140, 410-417), the pH dependence of acetate complexation has been revealed. It shows that acetate forms inner-sphere complexes on (110) in a very limited mildly acidic pH range while it can complex on (010) in the whole common pH range. The results presented in this study form a physical basis for understanding the geochemical processes involving clay-organics interactions.
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Affiliation(s)
- Xiandong Liu
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210093, P. R. China.
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23
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Mukherji D, Wagner M, Watson MD, Winzen S, de Oliveira TE, Marques CM, Kremer K. Relating side chain organization of PNIPAm with its conformation in aqueous methanol. SOFT MATTER 2016; 12:7995-8003. [PMID: 27605060 DOI: 10.1039/c6sm01789d] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Combining nuclear magnetic resonance (NMR), dynamic light scattering (DLS), and μs long all-atom simulations with two million particles, we establish a delicate correlation between increased side chain organization of PNIPAm and its collapse in aqueous methanol mixtures. We find that the preferential binding of methanol with PNIPAm side chains, bridging distal monomers along the polymer backbone, results in increased organization. Furthermore, methanol-PNIPAm preferential binding is dominated by hydrogen bonding. Our findings reveal that the collapse of PNIPAm is dominated by enthalpic interactions and that the standard poor solvent (entropic) effects play no major role.
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Affiliation(s)
- Debashish Mukherji
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany.
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24
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Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study. J Mol Model 2016; 22:210. [DOI: 10.1007/s00894-016-3075-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/27/2016] [Indexed: 11/26/2022]
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25
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Daily MD, Baer MD, Mundy CJ. Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer. J Phys Chem B 2016; 120:2198-208. [DOI: 10.1021/acs.jpcb.5b12277] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael D. Daily
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Marcel D. Baer
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher J. Mundy
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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26
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Baer MD, Mundy CJ. Local Aqueous Solvation Structure Around Ca2+ During Ca2+···Cl– Pair Formation. J Phys Chem B 2016; 120:1885-93. [DOI: 10.1021/acs.jpcb.5b09579] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcel D. Baer
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher J. Mundy
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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27
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Jamali AA, Ferdousi R, Razzaghi S, Li J, Safdari R, Ebrahimie E. DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins. Drug Discov Today 2016; 21:718-24. [PMID: 26821132 DOI: 10.1016/j.drudis.2016.01.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/05/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022]
Abstract
Application of computational methods in drug discovery has received increased attention in recent years as a way to accelerate drug target prediction. Based on 443 sequence-derived protein features, we applied the most commonly used machine learning methods to predict whether a protein is druggable as well as to opt for superior algorithm in this task. In addition, feature selection procedures were used to provide the best performance of each classifier according to the optimum number of features. When run on all features, Neural Network was the best classifier, with 89.98% accuracy, based on a k-fold cross-validation test. Among all the algorithms applied, the optimum number of most-relevant features was 130, according to the Support Vector Machine-Feature Selection (SVM-FS) algorithm. This study resulted in the discovery of new drug target which potentially can be employed in cell signaling pathways, gene expression, and signal transduction. The DrugMiner web tool was developed based on the findings of this study to provide researchers with the ability to predict druggable proteins. DrugMiner is freely available at www.DrugMiner.org.
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Affiliation(s)
- Ali Akbar Jamali
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ferdousi
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Razzaghi
- Information Technology Center, The University of Zanjan, Zanjan, Iran
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia
| | - Reza Safdari
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
| | - Esmaeil Ebrahimie
- School of Information Technology and Mathematical Sciences, Division of Information Technology, Engineering and the Environment, The University of South Australia, Adelaide, SA, Australia; Department of Genetics & Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia; School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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28
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de Oliveira TE, Netz PA, Mukherji D, Kremer K. Why does high pressure destroy co-non-solvency of PNIPAm in aqueous methanol? SOFT MATTER 2015; 11:8599-8604. [PMID: 26381828 DOI: 10.1039/c5sm01772f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
It is well known that poly(N-isopropylacrylamide) (PNIPAm) exhibits an interesting, yet puzzling, phenomenon of co-non-solvency. Co-non-solvency occurs when two competing good solvents for PNIPAm, such as water and alcohol, are mixed together. As a result, the same PNIPAm collapses within intermediate mixing ratios. This complex conformational transition is driven by preferential binding of methanol with PNIPAm. Interestingly, co-non-solvency can be destroyed when applying high hydrostatic pressures. In this work, using a large scale molecular dynamics simulation employing high pressures, we propose a microscopic picture behind the suppression of the co-non-solvency phenomenon. Based on thermodynamic and structural analysis, our results suggest that the preferential binding of methanol with PNIPAm gets partially lost at high pressures, making the background fluid reasonably homogeneous for the polymer. This is consistent with the hypothesis that the co-non-solvency phenomenon is driven by preferential binding and is not based on depletion effects.
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Affiliation(s)
- Tiago E de Oliveira
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany. and Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo A Netz
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany. and Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Debashish Mukherji
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany.
| | - Kurt Kremer
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany.
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29
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Church AT, Hughes ZE, Walsh TR. Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22* parameters. RSC Adv 2015. [DOI: 10.1039/c5ra11268k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We show that the CHARMM22* force-field over-binds the interaction between aqueous carboxylates and Ca2+, and introduce a modification that can recover experimentally-determined binding free energies for these systems.
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Affiliation(s)
- Andrew T. Church
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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30
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Kahlen J, Peter C, Donadio D. Molecular simulation of oligo-glutamates in a calcium-rich aqueous solution: insights into peptide-induced polymorph selection. CrystEngComm 2015. [DOI: 10.1039/c5ce00676g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advanced simulation methods show how glutamate oligomers prestructure Ca ions and induce structural motifs in correspondence with calciumoxalate pseudopolymorphs.
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Affiliation(s)
- Jens Kahlen
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
| | - Christine Peter
- University of Konstanz
- Department of Chemistry
- 78457 Konstanz, Germany
| | - Davide Donadio
- Max Planck Institute for Polymer Research
- 55128 Mainz, Germany
- Donostia International Physics Center
- 20018 San Sebastian, Spain
- Ikerbasque
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Jain A, Jochum M, Peter C. Molecular dynamics simulations of peptides at the air-water interface: influencing factors on peptide-templated mineralization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15486-15495. [PMID: 25470652 DOI: 10.1021/la503549q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biomineralization is the intricate, biomedically highly relevant process by which living organisms deposit minerals on biological matrices to stiffen tissues and build skeletal structures and shells. Rapaport and coworkers ( J. Am. Chem. Soc. 2000 , 122 , 12523 ; Adv. Funct. Mater. 2008 , 18 , 2889 ; Acta Biomater. 2012 , 8 , 2466 ) have designed a class of self-assembling amphiphilic peptides that are capable of forming hydrogels and attracting ions from the environment, generating structures akin to the extracellular matrix and promoting bone regeneration. The air-water interface serves both in experiment and in simulations as a model hydrophobic surface to mimic the cell's organic-aqueous interface and to investigate the organization of the peptide matrix into ordered β-pleated monolayers and the subsequent onset of biomineral formation. To obtain insight into the underlying molecular mechanism, we have used molecular dynamics simulations to study the effect of peptide sequence on aggregate stability and ion-peptide interactions. We find-in excellent agreement with experimental observations-that the nature of the peptide termini (proline vs phenylalanine) affect the aggregate order, while the nature of the acidic side chains (aspartic vs glutamic acid) affect the aggregate's stability in the presence of ions. These simulations provide valuable microscopic insight into the way ions and peptide templates mutually affect each other during the early stages of biomineralization preceding nucleation.
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Affiliation(s)
- Alok Jain
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
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Xue Y, Yuwen T, Zhu F, Skrynnikov NR. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry 2014; 53:6473-95. [PMID: 25207671 DOI: 10.1021/bi500904f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their structured targets. To obtain insight into the mechanism of formation of the electrostatic encounter complex, we investigated the binding of the peptide Sos (PPPVPPRRRR), which serves as a minimal model for an IDP, to the c-Crk N-terminal SH3 domain. Initially, we measured ¹⁵N relaxation rates at two magnetic field strengths and determined the binding shifts for the complex of Sos with wild-type SH3. We have also recorded a 3 μs molecular dynamics (MD) trajectory of this complex using the Amber ff99SB*-ILDN force field. The comparison of the experimental and simulated data shows that MD simulation consistently overestimates the strength of salt bridge interactions at the binding interface. The series of simulations using other advanced force fields also failed to produce any satisfactory results. To address this issue, we have devised an empirical correction to the Amber ff99SB*-ILDN force field whereby the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across the Arg-to-Asp and Arg-to-Glu salt bridges has been increased by 3%. Implementing this correction resulted in a good agreement between the simulations and the experiment. Adjusting the strength of salt bridge interactions removed a certain amount of strain contained in the original MD model, thus improving the binding of the hydrophobic N-terminal portion of the peptide. The arginine-rich C-terminal portion of the peptide, freed from the effect of the overstabilized salt bridges, was found to interconvert more rapidly between its multiple conformational states. The modified MD protocol has also been successfully used to simulate the entire binding process. In doing so, the peptide was initially placed high above the protein surface. It then arrived at the correct bound pose within ∼2 Å of the crystallographic coordinates. This simulation allowed us to analyze the details of the dynamic binding intermediate, i.e., the electrostatic encounter complex. However, an experimental characterization of this transient, weakly populated state remains out of reach. To overcome this problem, we designed the double mutant of c-Crk N-SH3 in which mutations Y186L and W169F abrogate tight Sos binding and shift the equilibrium toward the intermediate state resembling the electrostatic encounter complex. The results of the combined NMR and MD study of this engineered system will be reported in the next part of this paper.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
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