1
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Christ HA, Daniel NP, Solarczek J, Fresenborg LS, Schallmey A, Menzel H. Application of electrospun chitosan-based nanofibers as immobilization matrix for biomolecules. Appl Microbiol Biotechnol 2023; 107:7071-7087. [PMID: 37755509 PMCID: PMC10638201 DOI: 10.1007/s00253-023-12777-w] [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: 05/31/2023] [Revised: 08/02/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Nanofiber meshes from electrospun chitosan, highly modified with biotin and arylazides, are well-suited for application as enzyme immobilization matrices. To test this, catalytically active biomolecules were immobilized onto photocrosslinked nanofibrous nonwovens consisting mainly of biotinylated fungal chitosan and a small amount (10 w%) of poly ethylene oxide. In this study, we show that over 10 μg eugenol oxidase per milligram dry polymer matrix can be loaded on UV-crosslinked chitosan nanofibers. We further demonstrate that bound enzyme activity can be fully retained for over 7 days of storage at ambient conditions in aqueous buffer. Samples loaded at maximum enzyme carrying capacity were tested in a custom-made plug-flow reactor system with online UV-VIS spectroscopy for activity determination. High wettability and durability of the hydrophilic chitosan support matrix enabled continuous oxidation of model substrate vanillyl alcohol into vanillin with constant turnover at flow rates of up to 0.24 L/h for over 6 h. This proves the above hypothesis and enables further application of the fibers as stacked microfluidic membranes, biosensors, or structural starting points for affinity crosslinked enzyme gels. KEY POINTS: • Biotinylated chitosan-based nanofibers retain enzymes via mild affinity interactions • Immobilized eugenol oxidase shows high activity and resists continuous washing • Nanofiber matrix material tolerated high flow rates in a continuous-flow setup.
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Affiliation(s)
- Henrik-Alexander Christ
- Institute for Technical Chemistry, Braunschweig University of Technology, Hagenring 30, 38106, Braunschweig, Germany
| | - Nils Peter Daniel
- Institute for Biochemistry, Braunschweig University of Technology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Jennifer Solarczek
- Institute for Biochemistry, Braunschweig University of Technology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Leonard Sebastian Fresenborg
- Department of Molecular Cell Biology of Plants, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Anett Schallmey
- Institute for Biochemistry, Braunschweig University of Technology, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Henning Menzel
- Institute for Technical Chemistry, Braunschweig University of Technology, Hagenring 30, 38106, Braunschweig, Germany.
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2
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Govind Kumar V, Polasa A, Agrawal S, Kumar TKS, Moradi M. Binding affinity estimation from restrained umbrella sampling simulations. NATURE COMPUTATIONAL SCIENCE 2023; 3:59-70. [PMID: 38177953 PMCID: PMC10766565 DOI: 10.1038/s43588-022-00389-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2024]
Abstract
The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a combination thereof. Here we discuss a purely physics-based sampling approach based on biased molecular dynamics simulations. Our proposed method generalizes and simplifies previously suggested stratification strategies that use umbrella sampling or other enhanced sampling simulations with additional collective-variable-based restraints. The approach presented here uses a flexible scheme that can be easily tailored for any system of interest. We estimate the binding affinity of human fibroblast growth factor 1 to heparin hexasaccharide based on the available crystal structure of the complex as the initial model and four different variations of the proposed method to compare against the experimentally determined binding affinity obtained from isothermal titration calorimetry experiments.
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Affiliation(s)
- Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Shilpi Agrawal
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | | | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
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3
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Kliuchnikov E, Klyshko E, Kelly MS, Zhmurov A, Dima RI, Marx KA, Barsegov V. Microtubule assembly and disassembly dynamics model: Exploring dynamic instability and identifying features of Microtubules' Growth, Catastrophe, Shortening, and Rescue. Comput Struct Biotechnol J 2022; 20:953-974. [PMID: 35242287 PMCID: PMC8861655 DOI: 10.1016/j.csbj.2022.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/21/2022] Open
Abstract
Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at the molecular level are not understood. We developed a 3D Microtubule Assembly and Disassembly DYnamics (MADDY) model, based upon a bead-per-monomer representation of the αβ-tubulin dimers forming an MT lattice, stabilized by the lateral and longitudinal interactions between tubulin subunits. The model was parameterized against the experimental rates of MT growth and shortening, and pushing forces on the Dam1 protein complex due to protofilaments splaying out. Using the MADDY model, we carried out GPU-accelerated Langevin simulations to access dynamic instability behavior. By applying Machine Learning techniques, we identified the MT characteristics that distinguish simultaneously all four kinetic states: growth, catastrophe, shortening, and rescue. At the cellular 25 μM tubulin concentration, the most important quantities are the MT length L , average longitudinal curvatureκ long , MT tip width w , total energy of longitudinal interactions in MT latticeU long , and the energies of longitudinal and lateral interactions required to complete MT to full cylinderU long add andU lat add . At high 250 μM tubulin concentration, the most important characteristics are L ,κ long , number of hydrolyzed αβ-tubulin dimersn hyd and number of lateral interactions per helical pitchn lat in MT lattice, energy of lateral interactions in MT latticeU lat , and energy of longitudinal interactions in MT tipu long . These results allow greater insights into what brings about kinetic state stability and the transitions between states involved in MT dynamic instability behavior.
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Affiliation(s)
| | - Eugene Klyshko
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Maria S. Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Artem Zhmurov
- KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ruxandra I. Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Kenneth A. Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA
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4
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Chen LY. Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions. FRONTIERS IN PHYSICS 2020; 8:202. [PMID: 32542181 PMCID: PMC7295167 DOI: 10.3389/fphy.2020.00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249 U.S.A
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5
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Fingernagel J, Boye S, Kietz A, Höbel S, Wozniak K, Moreno S, Janke A, Lederer A, Aigner A, Temme A, Voit B, Appelhans D. Mono- and Polyassociation Processes of Pentavalent Biotinylated PEI Glycopolymers for the Fabrication of Biohybrid Structures with Targeting Properties. Biomacromolecules 2019; 20:3408-3424. [DOI: 10.1021/acs.biomac.9b00667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes Fingernagel
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Susanne Boye
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
| | - André Kietz
- Clinical Pharmacology, Faculty of Medicine, Rudolf-Boehm-Institute of Pharmacology and Toxicology, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Sabrina Höbel
- Clinical Pharmacology, Faculty of Medicine, Rudolf-Boehm-Institute of Pharmacology and Toxicology, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Katarzyna Wozniak
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
| | - Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
| | - Andreas Janke
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
| | - Albena Lederer
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Achim Aigner
- Clinical Pharmacology, Faculty of Medicine, Rudolf-Boehm-Institute of Pharmacology and Toxicology, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Achim Temme
- Experimental Neurosurgery/Tumor Immunology, TU Dresden, D-01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner site Dresden, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Strasse 6, D-01069 Dresden, Germany
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6
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Mondarte EA, Maekawa T, Nyu T, Tahara H, Lkhamsuren G, Hayashi T. Detection of streptavidin-biotin intermediate metastable states at the single-molecule level using high temporal-resolution atomic force microscopy. RSC Adv 2019; 9:22705-22712. [PMID: 35519498 PMCID: PMC9067134 DOI: 10.1039/c9ra04106k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/18/2019] [Indexed: 11/21/2022] Open
Abstract
Although the streptavidin-biotin intermolecular bond has been extensively used in many applications due to its high binding affinity, its exact nature and interaction mechanism have not been well understood. Several reports from previous studies gave a wide range of results in terms of the system's energy potential landscape because of bypassing some short-lived states in the detection process. We employed a quasi-static process of slowly loading force onto the bond (loading rate = 20 pN s-1) to minimize the force-induced disruption and to provide a chance to explore the system in near-equilibrium. Therein, by utilizing a fast sampling rate for the detection of force by atomic force microscopy (20 μs per data point), several transient states of the system were clearly resolved in our force spectroscopy measurements. These key strategies allow the determination of the states' relative positions and free energy levels along the pulling reaction coordinate for the illustration of an energy landscape of the system.
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Affiliation(s)
- Evan Angelo Mondarte
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
| | - Tatsuhiro Maekawa
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
| | - Takashi Nyu
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
| | - Hiroyuki Tahara
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
| | - Ganchimeg Lkhamsuren
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
| | - Tomohiro Hayashi
- Tokyo Institute of Technology, Department of Materials Science and Engineering, School of Materials and Chemical Technology 4259 Nagatsuta-cho, Midori-ku Yokohama Kanagawa 226-8503 Japan
- JST-PRESTO 4-1-8 Hon-cho Kawaguchi Saitama 332-0012 Japan
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7
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Delgadillo RF, Mueser TC, Zaleta-Rivera K, Carnes KA, González-Valdez J, Parkhurst LJ. Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin. PLoS One 2019; 14:e0204194. [PMID: 30818336 PMCID: PMC6394990 DOI: 10.1371/journal.pone.0204194] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.
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Affiliation(s)
- Roberto F. Delgadillo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, United States of America
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, United States of America
| | - Katie A. Carnes
- GlaxoSmithKline, Medicinal Science and Technology, R&D, King of Prussia, Pennsylvania, United States of America
| | - José González-Valdez
- Tecnologico de Monterrey, School of Engineering and Science, NL, Monterrey, Mexico
| | - Lawrence J. Parkhurst
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
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8
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Yenjai S, Kumar CV, Kuno M, Liwporncharoenvong T, Samosorn S, Buranaprapuk A. Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2018; 186:23-30. [PMID: 29990670 DOI: 10.1016/j.jphotobiol.2018.07.001] [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: 03/10/2018] [Revised: 06/08/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV-Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (Kb) of 6.2 × 105, 6.7 × 105 and 4.6 × 105 M-1, respectively. No significant changes of Stern-Volmer quenching constant (Ksv) with Co(NH3)6Cl3 has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH3)6Cl3, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed Ksv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77-78, was within 5 Å of the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site.
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Affiliation(s)
- Sudarat Yenjai
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Challa V Kumar
- Department of Chemistry, 55 N. Eagleville Road, University of Connecticut, Storrs, CT 06269-3060, USA; Department of Molecular and Cellular Biology, 91 N. Eagleville Road, U-3125, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Mayuso Kuno
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | - Siritron Samosorn
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
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9
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Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Biochem Biophys Res Commun 2016; 483:203-208. [PMID: 28034750 DOI: 10.1016/j.bbrc.2016.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/24/2016] [Indexed: 12/25/2022]
Abstract
Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity---pulling out the ligand---closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature.
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10
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Changede R, Sheetz M. Integrin and cadherin clusters: A robust way to organize adhesions for cell mechanics. Bioessays 2016; 39:1-12. [PMID: 27930828 DOI: 10.1002/bies.201600123] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies at the nanometer scale have revealed that relatively uniform clusters of adhesion proteins (50-100 nm) constitute the modular units of cell adhesion sites in both cell-matrix and cell-cell adhesions. Super resolution microscopy and membrane protein diffusion studies both suggest that even large focal adhesions are formed of 100 nm clusters that are loosely aggregated. Clusters of 20-50 adhesion molecules (integrins or cadherins) can support large forces through avidity binding interactions but can also be disassembled or endocytosed rapidly. Assembly of the clusters of integrins is force-independent and involves gathering integrins at ligand binding sites where they are stabilized by cytoplasmic adhesion proteins that crosslink the integrin cytoplasmic tails plus connect the clusters to the cell cytoskeleton. Cooperative-signaling events can occur in a single cluster without cascading to other clusters. Thus, the clusters appear to be very important elements in many cellular processes and can be considered as a critical functional module.
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Affiliation(s)
- Rishita Changede
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Michael Sheetz
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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11
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Chen LY. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate. J Chem Theory Comput 2016; 11:1928-38. [PMID: 25937822 PMCID: PMC4411208 DOI: 10.1021/ct501162f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Indexed: 01/10/2023]
Abstract
![]()
Computing
the free energy of binding a ligand to a protein is a
difficult task of essential importance for which purpose various theoretical/computational
approaches have been pursued. In this paper, we develop a hybrid steered
molecular dynamics (hSMD) method capable of resolving one ligand–protein
complex within a few wall-clock days with high enough accuracy to
compare with the experimental data. This hSMD approach is based on
the relationship between the binding affinity and the potential of
mean force (PMF) in the established literature. It involves simultaneously
steering n (n = 1, 2, 3, ...) centers
of mass of n selected segments of the ligand using n springs of infinite stiffness. Steering the ligand from
a single initial state chosen from the bound state ensemble to the
corresponding dissociated state, disallowing any fluctuations of the
pulling centers along the way, one can determine a 3n-dimensional PMF curve connecting the two states by sampling a small
number of forward and reverse pulling paths. This PMF constitutes
a large but not the sole contribution to the binding free energy.
Two other contributors are (1) the partial partition function containing
the equilibrium fluctuations of the ligand at the binding site and
the deviation of the initial state from the PMF minimum and (2) the
partial partition function containing rotation and fluctuations of
the ligand around one of the pulling centers that is fixed at a position
far from the protein. We implement this hSMD approach for two ligand–protein
complexes whose structures were determined and whose binding affinities
were measured experimentally: caprylic acid binding to bovine β-lactoglobulin
and glutathione binding to Schistosoma japonicum glutathione S-transferase tyrosine 7 to phenylalanine mutant. Our computed
binding affinities agree with the experimental data within a factor
of 1.5. The total time of computation for these two all-atom model
systems (consisting of 96K and 114K atoms, respectively) was less
than one wall-clock week using 512 cores (32 Xeon E5-2680 processors).
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12
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Rodriguez RA, Yu L, Chen LY. Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics. J Chem Theory Comput 2016; 11:4427-4438. [PMID: 26366131 DOI: 10.1021/acs.jctc.5b00340] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Computing protein-protein association affinities is one of the fundamental challenges in computational biophysics/biochemistry. The overwhelming amount of statistics in the phase space of very high dimensions cannot be sufficiently sampled even with today's high-performance computing power. In this article, we extend a potential of mean force (PMF)-based approach, the hybrid steered molecular dynamics (hSMD) approach we developed for ligand-protein binding, to protein-protein association problems. For a protein complex consisting of two protomers, P1 and P2, we choose m (≥3) segments of P1 whose m centers of mass are to be steered in a chosen direction and n (≥3) segments of P2 whose n centers of mass are to be steered in the opposite direction. The coordinates of these m + n centers constitute a phase space of 3(m + n) dimensions (3(m + n)D). All other degrees of freedom of the proteins, ligands, solvents, and solutes are freely subject to the stochastic dynamics of the all-atom model system. Conducting SMD along a line in this phase space, we obtain the 3(m + n)D PMF difference between two chosen states: one single state in the associated state ensemble and one single state in the dissociated state ensemble. This PMF difference is the first of four contributors to the protein-protein association energy. The second contributor is the 3(m + n - 1)D partial partition in the associated state accounting for the rotations and fluctuations of the (m + n - 1) centers while fixing one of the m + n centers of the P1-P2 complex. The two other contributors are the 3(m - 1)D partial partition of P1 and the 3(n - 1)D partial partition of P2 accounting for the rotations and fluctuations of their m - 1 or n - 1 centers while fixing one of the m/n centers of P1/P2 in the dissociated state. Each of these three partial partitions can be factored exactly into a 6D partial partition in multiplication with a remaining factor accounting for the small fluctuations while fixing three of the centers of P1, P2, or the P1-P2 complex, respectively. These small fluctuations can be well-approximated as Gaussian, and every 6D partition can be reduced in an exact manner to three problems of 1D sampling, counting the rotations and fluctuations around one of the centers as being fixed. We implement this hSMD approach to the Ras-RalGDS complex, choosing three centers on RalGDS and three on Ras (m = n = 3). At a computing cost of about 71.6 wall-clock hours using 400 computing cores in parallel, we obtained the association energy, -9.2 ± 1.9 kcal/mol on the basis of CHARMM 36 parameters, which well agrees with the experimental data, -8.4 ± 0.2 kcal/mol.
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Affiliation(s)
- Roberto A Rodriguez
- Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249 USA
| | - Lili Yu
- Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249 USA
| | - Liao Y Chen
- Department of Physics, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249 USA
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13
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Kassem S, Ahmed M, El-Sheikh S, Barakat KH. Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods. J Mol Graph Model 2015; 62:105-117. [PMID: 26407139 DOI: 10.1016/j.jmgm.2015.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/06/2015] [Accepted: 09/10/2015] [Indexed: 11/17/2022]
Abstract
Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.
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Affiliation(s)
- Summer Kassem
- Department of Physics, American University in Cairo, Cairo, Egypt
| | - Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Salah El-Sheikh
- Department of Physics, American University in Cairo, Cairo, Egypt
| | - Khaled H Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, Canada.
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14
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Chen LY. Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach. Mol Membr Biol 2015; 32:19-25. [PMID: 25955791 DOI: 10.3109/09687688.2015.1006275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to elucidate how phosphatidylserine (PS6) interacts with AQP5 in a cell membrane, we developed a hybrid steered molecular dynamics (hSMD) method that involved: (1) Simultaneously steering two centers of mass of two selected segments of the ligand, and (2) equilibrating the ligand-protein complex with and without biasing the system. Validating hSMD, we first studied vascular endothelial growth factor receptor 1 (VEGFR1) in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide (8ST), for which the binding energy is known from in vitro experiments. In this study, our computed binding energy well agreed with the experimental value. Knowing the accuracy of this hSMD method, we applied it to the AQP5-lipid-bilayer system to answer an outstanding question relevant to AQP5's physiological function: Will the PS6, a lipid having a single long hydrocarbon tail that was found in the central pore of the AQP5 tetramer crystal, actually bind to and inhibit AQP5's central pore under near-physiological conditions, namely, when AQP5 tetramer is embedded in a lipid bilayer? We found, in silico, using the CHARMM 36 force field, that binding PS6 to AQP5 was a factor of 3 million weaker than "binding" it in the lipid bilayer. This suggests that AQP5's central pore will not be inhibited by PS6 or a similar lipid in a physiological environment.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas , USA
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15
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Molla MR, Rangadurai P, Pavan GM, Thayumanavan S. Experimental and theoretical investigations in stimuli responsive dendrimer-based assemblies. NANOSCALE 2015; 7:3817-37. [PMID: 25260107 PMCID: PMC4336240 DOI: 10.1039/c4nr04563g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stimuli-responsive macromolecular assemblies are of great interest in drug delivery applications, as it holds the promise to keep the drug molecules sequestered under one set of conditions and release them under another. The former set of conditions could represent circulation, while the latter could represent a disease location. Over the past two decades, sizeable contributions to this field have come from dendrimers, which along with their monodispersity, provide great scope for structural modifications at the molecular level. In this paper, we briefly discuss the various synthetic strategies that have been developed so far to obtain a range of functional dendrimers. We then discuss the design strategies utilized to introduce stimuli responsive elements within the dendritic architecture. The stimuli itself are broadly classified into two categories, viz. extrinsic and intrinsic. Extrinsic stimuli are externally induced such as temperature and light variations, while intrinsic stimuli involve physiological aberrations such as variations in pH, redox conditions, proteins and enzyme concentrations in pathological tissues. Furthermore, the unique support from molecular dynamics (MD) simulations has been highlighted. MD simulations have helped back many of the observations made from assembly formation properties to rationalized the mechanism of drug release and this has been illustrated with discussions on G4 PPI (Poly propylene imine) dendrimers and biaryl facially amphiphilic dendrimers. The synergy that exists between experimental and theoretical studies open new avenues for the use of dendrimers as versatile drug delivery systems.
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Affiliation(s)
- Mijanur Rahaman Molla
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA. Fax: + 1 413 545 4490; Tel: + 1 413 545 1313
| | - Poornima Rangadurai
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA. Fax: + 1 413 545 4490; Tel: + 1 413 545 1313
| | - Giovanni M. Pavan
- Department of Innovative Technologies, University of Applied Science of Southern Switzerland, Galleria 2, Manno 6928, Switzerland. Tel: + 41 58 666 6676
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA. Fax: + 1 413 545 4490; Tel: + 1 413 545 1313
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Liu J, Wang X, Zhang JZH, He X. Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method. RSC Adv 2015. [DOI: 10.1039/c5ra20185c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An efficient fragment-based quantum mechanical method has been successfully applied for reliable prediction of protein–ligand binding affinities.
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Affiliation(s)
- Jinfeng Liu
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
| | - Xianwei Wang
- Center for Optics & Optoelectronics Research
- College of Science
- Zhejiang University of Technology
- Hangzhou
- China
| | - John Z. H. Zhang
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
| | - Xiao He
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- College of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
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17
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Jurchenko C, Chang Y, Narui Y, Zhang Y, Salaita KS. Integrin-generated forces lead to streptavidin-biotin unbinding in cellular adhesions. Biophys J 2014; 106:1436-46. [PMID: 24703305 DOI: 10.1016/j.bpj.2014.01.049] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 12/20/2013] [Accepted: 01/29/2014] [Indexed: 11/18/2022] Open
Abstract
The interplay between chemical and mechanical signals plays an important role in cell biology, and integrin receptors are the primary molecules involved in sensing and transducing external mechanical cues. We used integrin-specific probes in molecular tension fluorescence microscopy to investigate the pN forces exerted by integrin receptors in living cells. The molecular tension fluorescence microscopy probe consisted of a cyclic Arg-Gly-Asp-D-Phe-Lys(Cys) (cRGDfK(C)) peptide tethered to the terminus of a polyethylene glycol polymer that was attached to a surface through streptavidin-biotin linkage. A fluorescence resonance energy transfer mechanism was used to visualize tension-driven extension of the polymer. Surprisingly, we found that integrin receptors dissociate streptavidin-biotin tethered ligands in focal adhesions within 60 min of cell seeding. Although streptavidin-biotin binding affinity is described as the strongest noncovalent bond in nature, and is ~10(6) - 10(8) times larger than that of integrin-RGD affinity, our results suggest that individual integrin-ligand complexes undergo a marked enhancement in stability when the receptor assembles in the cell membrane. Based on the observation of streptavidin-biotin unbinding, we also conclude that the magnitude of integrin-ligand tension in focal adhesions can reach values that are at least 10 fold larger than was previously estimated using traction force microscopy-based methods.
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Affiliation(s)
| | - Yuan Chang
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Yoshie Narui
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Yun Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia
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Amado Torres D, Garzoni M, Subrahmanyam AV, Pavan GM, Thayumanavan S. Protein-triggered supramolecular disassembly: insights based on variations in ligand location in amphiphilic dendrons. J Am Chem Soc 2014; 136:5385-99. [PMID: 24641469 PMCID: PMC4004214 DOI: 10.1021/ja500634u] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Indexed: 12/14/2022]
Abstract
We use monodisperse dendrons that allow control over functional group presentation to investigate the influence of the location of a ligand on protein-induced disassembly and release of encapsulated small molecules. Based on both experiments and molecular dynamics simulations, we demonstrate that ligand location greatly influences release of guest molecules from the dendron-based supramolecular assembly. We show that a ligand moiety grafted to the dendron periphery is more accessible for the target protein in aqueous solution. On the other hand, the ligand moiety placed at the focal point or at the intermediate layer within the dendritic scaffold is less accessible, since it is surrounded by an environment rich in PEG chains, which hinders binding and even influences nonspecific interactions. We also demonstrate that the specific binding between one ligand and the target protein can destabilize the dendritic assembly. Furthermore, if more ligands are available, multivalent interactions are also possible with extravidin, which speed up disassembly and trigger the release of hydrophobic guests.
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Affiliation(s)
- Diego Amado Torres
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Matteo Garzoni
- Department
of Innovative Technologies, University of
Applied Science of Southern Switzerland, Manno 6928, Switzerland
| | - Ayyagari V. Subrahmanyam
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Giovanni M. Pavan
- Department
of Innovative Technologies, University of
Applied Science of Southern Switzerland, Manno 6928, Switzerland
| | - S. Thayumanavan
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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19
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General IJ, Meirovitch H. Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field. J Chem Theory Comput 2013; 9:4609-19. [PMID: 26589173 DOI: 10.1021/ct400484u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating ΔA(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, ΔA(0) is obtained in a new way as a sum of several components, among them is ΔSligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where ΔSligand might be significant. Technically, one should verify that the results for ΔSligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where ΔA(0) = -12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained ΔA(0) = -13.6 ± 1.1, -16.6 ± 1.4, and -16.7 ± 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for ΔA(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3) has led to the experimental ΔA(0) in the [0.2,2] ns region close to the crystal structure. Keeping the complex near its crystal structure has been a successful approach in the literature. To check this avenue further, we applied harmonic restraints on backbone atoms and obtained unsatisfactory results for ΔA(0), suggesting that implementation of this approach is not straightforward. Converging results for ΔSligand were obtained in all regions, where the result ΔSligand([0.2,2]) = 7.1 ± 1.2 kcal/mol is less region dependent than ΔA(0) and is relatively large probably due to the large ligand.
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Affiliation(s)
- Ignacio J General
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , 3059 BST3, Pittsburgh, Pennsylvania 15260, United States
| | - Hagai Meirovitch
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , 3059 BST3, Pittsburgh, Pennsylvania 15260, United States.,Department of Physics, Bar-Ilan University , Ramat Gan, 52900, Israel
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Gumbart JC, Roux B, Chipot C. Standard binding free energies from computer simulations: What is the best strategy? J Chem Theory Comput 2012; 9:794-802. [PMID: 23794960 DOI: 10.1021/ct3008099] [Citation(s) in RCA: 239] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Accurate prediction of standard binding free energies describing protein:ligand association remains a daunting computational endeavor. This challenge is rooted to a large extent in the considerable changes in conformational, translational and rotational entropies underlying the binding process that atomistic simulations cannot easily capture. In spite of significant methodological advances, reflected in a continuously improving agreement with experiment, a characterization of alternate strategies aimed at measuring binding affinities, notably their respective advantages and drawbacks, is somewhat lacking. Here, two distinct avenues to determine the standard binding free energy are compared in the case of a short, proline-rich peptide associating to the Src homology domain 3 of tyrosine kinase Abl. These avenues - one relying upon alchemical transformations and the other on potentials of mean force (PMFs) - invoke a series of geometrical restraints acting on collective variables designed to alleviate sampling limitations inherent to classical molecular dynamics simulations. The experimental binding free energy of ΔGbind = -7.99 kcal/mol is well reproduced by the two strategies developed herein, with ΔGbind = -7.7 for the alchemical route and ΔGbind = -7.8 kcal/mol for the alternate PMF-based route. In detailing the underpinnings of these numerical strategies devised for the accurate determination of standard binding free energies, many practical elements of the proposed rigorous, conceptual framework are clarified, thereby paving way to tackle virtually any recognition and association phenomenon.
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Affiliation(s)
- James C Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana IL 61801
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