1
|
Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
Collapse
Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
| |
Collapse
|
2
|
Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
Collapse
Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
| |
Collapse
|
3
|
Wales DJ. Energy Landscapes and Heat Capacity Signatures for Monomers and Dimers of Amyloid-Forming Hexapeptides. Int J Mol Sci 2023; 24:10613. [PMID: 37445791 DOI: 10.3390/ijms241310613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Amyloid formation is a hallmark of various neurodegenerative disorders. In this contribution, energy landscapes are explored for various hexapeptides that are known to form amyloids. Heat capacity (CV) analysis at low temperature for these hexapeptides reveals that the low energy structures contributing to the first heat capacity feature above a threshold temperature exhibit a variety of backbone conformations for amyloid-forming monomers. The corresponding control sequences do not exhibit such structural polymorphism, as diagnosed via end-to-end distance and a dihedral angle defined for the monomer. A similar heat capacity analysis for dimer conformations obtained using basin-hopping global optimisation shows clear features in end-to-end distance versus dihedral correlation plots, where amyloid-forming sequences exhibit a preference for larger end-to-end distances and larger positive dihedrals. These results hold true for sequences taken from tau, amylin, insulin A chain, a de novo designed peptide, and various control sequences. While there is a little overall correlation between the aggregation propensity and the temperature at which the low-temperature CV feature occurs, further analysis suggests that the amyloid-forming sequences exhibit the key CV feature at a lower temperature compared to control sequences derived from the same protein.
Collapse
Affiliation(s)
- David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| |
Collapse
|
4
|
Jankovic B, Bozovic O, Hamm P. Addendum: Sensing the allosteric force. Nat Commun 2023; 14:2735. [PMID: 37173296 PMCID: PMC10182073 DOI: 10.1038/s41467-023-37893-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Affiliation(s)
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
5
|
Ortiz-Oliveros HB, Ouerfelli N, Cruz-Gonzalez D, Avila-Pérez P, Bulgariu L, Flaifel MH, Abouzeid FM. Modeling of the relationship between the thermodynamic parameters ΔH° and ΔS° with temperature in the removal of Pb ions in aqueous medium: Case study. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
6
|
Hammerschmidt SJ, Huber S, Braun NJ, Lander M, Steinmetzer T, Kersten C. Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs. Arch Pharm (Weinheim) 2022; 356:e2200518. [PMID: 36480352 DOI: 10.1002/ardp.202200518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.
Collapse
Affiliation(s)
- Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| |
Collapse
|
7
|
Leibiger B, Stapf M, Mazik M. Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms. Molecules 2022; 27:7630. [PMID: 36364458 PMCID: PMC9654292 DOI: 10.3390/molecules27217630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 09/29/2023] Open
Abstract
The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards β-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.
Collapse
Affiliation(s)
| | | | - Monika Mazik
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09596 Freiberg, Germany
| |
Collapse
|
8
|
Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
Collapse
Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
| |
Collapse
|
9
|
Eskew MW, Benight AS. Equivalence of the transition heat capacities of proteins and DNA. Biochem Biophys Res Commun 2022; 597:98-101. [PMID: 35134611 DOI: 10.1016/j.bbrc.2022.01.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023]
Abstract
It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.
Collapse
Affiliation(s)
- Matthew W Eskew
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA.
| | - Albert S Benight
- ThermoCap Laboratories Inc, Portland, OR, USA; Department of Chemistry, Portland State University, Portland, OR, USA; Department of Physics, Portland State University, Portland, OR, USA
| |
Collapse
|
10
|
Ritt CL, Liu M, Pham TA, Epsztein R, Kulik HJ, Elimelech M. Machine learning reveals key ion selectivity mechanisms in polymeric membranes with subnanometer pores. SCIENCE ADVANCES 2022; 8:eabl5771. [PMID: 35030018 PMCID: PMC8759746 DOI: 10.1126/sciadv.abl5771] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Designing single-species selective membranes for high-precision separations requires a fundamental understanding of the molecular interactions governing solute transport. Here, we comprehensively assess molecular-level features that influence the separation of 18 different anions by nanoporous cellulose acetate membranes. Our analysis identifies the limitations of bulk solvation characteristics to explain ion transport, highlighted by the poor correlation between hydration energy and the measured permselectivity (R2 = 0.37). Entropy-enthalpy compensation, spanning 40 kilojoules per mole, leads to a free-energy barrier (∆G‡) variation of only ~8 kilojoules per mole across all anions. We apply machine learning to elucidate descriptors for energetic barriers from a set of 126 collected features. Notably, electrostatic features account for 75% of the overall features used to describe ∆G‡, despite the relatively uncharged state of cellulose acetate. Our work presents an approach for studying ion transport across nanoporous membranes that could enable the design of ion-selective membranes.
Collapse
Affiliation(s)
- Cody L. Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520-8286, USA
| | - Mingjie Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tuan Anh Pham
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Razi Epsztein
- Faculty of Civil and Environmental Engineering, Technion–Israel Institute of Technology, Haifa 32000, Israel
| | - Heather J. Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author. (M.E.); (H.J.K.)
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520-8286, USA
- Corresponding author. (M.E.); (H.J.K.)
| |
Collapse
|
11
|
Precupas A, Sandu R, Neculae AVF, Neacsu A, Popa VT. Calorimetric, spectroscopic and computational investigation of morin binding effect on bovine serum albumin stability. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Cabadaj M, Bashir S, Haskins D, Said J, McCoubrey L, Gaisford S, Beezer A. Kinetic analysis of microcalorimetric data derived from microbial growth: Basic theoretical, practical and industrial considerations. J Microbiol Methods 2021; 187:106276. [PMID: 34214601 DOI: 10.1016/j.mimet.2021.106276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/19/2022]
Abstract
We report here a mathematical framework for the quantitative interpretation of exponential bacterial growth measured with isothermal microcalorimetry. The method allows determination of many parameters that define the exponential growth phase. To automate the analysis, we also wrote a coding program, so that the approach could be embedded in a commercial setting. As an exemplar, we apply the method to a commercial probiotic product. The outcome was that we could identify characteristic parameters of growth (including rate constant and doubling time), and hence authenticate product quality, within 15 h. This compares favourably with the current 7-10 days required for conventional microbiological assessment (to allow release of product for bottling and marketing) via plating methods. The method would lend itself to growth analysis of single and mixed bacterial cultures.
Collapse
Affiliation(s)
- Miroslav Cabadaj
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; Symprove Ltd, Sandy Farm, The Sands, Farnham, Surrey, GU10 1PX, UK
| | - Shazia Bashir
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - David Haskins
- The Coach House, Polsted Lane, Compton, Surrey GU3 1JE, UK
| | - Jawal Said
- Cernotas Ltd, Sandy Farm, The Sands, Farnham, Surrey GU10 1PX, UK
| | - Laura McCoubrey
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK.
| | - Anthony Beezer
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| |
Collapse
|
13
|
Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
Collapse
Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
| | | |
Collapse
|
14
|
Sponga A, Arolas JL, Schwarz TC, Jeffries CM, Rodriguez Chamorro A, Kostan J, Ghisleni A, Drepper F, Polyansky A, De Almeida Ribeiro E, Pedron M, Zawadzka-Kazimierczuk A, Mlynek G, Peterbauer T, Doto P, Schreiner C, Hollerl E, Mateos B, Geist L, Faulkner G, Kozminski W, Svergun DI, Warscheid B, Zagrovic B, Gautel M, Konrat R, Djinović-Carugo K. Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with α-actinin. SCIENCE ADVANCES 2021; 7:eabg7653. [PMID: 34049882 PMCID: PMC8163081 DOI: 10.1126/sciadv.abg7653] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/13/2021] [Indexed: 05/03/2023]
Abstract
In sarcomeres, α-actinin cross-links actin filaments and anchors them to the Z-disk. FATZ (filamin-, α-actinin-, and telethonin-binding protein of the Z-disk) proteins interact with α-actinin and other core Z-disk proteins, contributing to myofibril assembly and maintenance. Here, we report the first structure and its cellular validation of α-actinin-2 in complex with a Z-disk partner, FATZ-1, which is best described as a conformational ensemble. We show that FATZ-1 forms a tight fuzzy complex with α-actinin-2 and propose an interaction mechanism via main molecular recognition elements and secondary binding sites. The obtained integrative model reveals a polar architecture of the complex which, in combination with FATZ-1 multivalent scaffold function, might organize interaction partners and stabilize α-actinin-2 preferential orientation in Z-disk. Last, we uncover FATZ-1 ability to phase-separate and form biomolecular condensates with α-actinin-2, raising the question whether FATZ proteins can create an interaction hub for Z-disk proteins through membraneless compartmentalization during myofibrillogenesis.
Collapse
Affiliation(s)
- Antonio Sponga
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Joan L Arolas
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Thomas C Schwarz
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | - Ariadna Rodriguez Chamorro
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Julius Kostan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Andrea Ghisleni
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
- National Research University Higher School of Economics, Moscow 101000, Russia
| | - Euripedes De Almeida Ribeiro
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Miriam Pedron
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Thomas Peterbauer
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Dr. BohrGasse 9, A-1030 Vienna, Austria
| | - Pierantonio Doto
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Claudia Schreiner
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Eneda Hollerl
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Leonhard Geist
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | | | - Wiktor Kozminski
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dmitri I Svergun
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Mathias Gautel
- King's College London BHF Centre for Research Excellence, Randall Centre for Cell and Molecular Biophysics, London SE1 1UL, UK
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
15
|
Gaardløs M, Samsonov SA, Sletmoen M, Hjørnevik M, Sætrom GI, Tøndervik A, Aachmann FL. Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4. Glycobiology 2021; 31:1616-1635. [PMID: 33822050 DOI: 10.1093/glycob/cwab025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/10/2021] [Indexed: 01/18/2023] Open
Abstract
Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues' roles in binding and movement along the alginate chains.
Collapse
Affiliation(s)
- Margrethe Gaardløs
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | | | - Marit Sletmoen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Maya Hjørnevik
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Gerd Inger Sætrom
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Anne Tøndervik
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands veg 3 B, N-7491 Trondheim, Norway
| | - Finn Lillelund Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| |
Collapse
|
16
|
Dos Santos Silva Araújo L, Lazzara G, Chiappisi L. Cyclodextrin/surfactant inclusion complexes: An integrated view of their thermodynamic and structural properties. Adv Colloid Interface Sci 2021; 289:102375. [PMID: 33592397 DOI: 10.1016/j.cis.2021.102375] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
Cyclodextrins (CDs) play an important role in self-assembly systems of amphiphiles. The structure of CDs provides distinguished physicochemical properties, including the ability to form host-guest complexes. The complexation affects the properties of guest molecules and can produce supramolecular aggregates with desirable characteristics for fundamental and practical applications. Surfactants are particularly attractive host molecules due to their wide variety, availability, responsiveness to different stimuli, and high relevance in different fields, e.g. medical, cosmetic, pharmaceutical, and food industries. The tendency of organization in higher-order supramolecular aggregates arises the interest in applying such versatile complexes in the development of novel materials. In this review, we provide a comprehensive overview of the thermodynamics aspects of surfactants and CDs inclusion complexes formation in aqueous environment, emphasizing the assessment of the interactions, thermodynamic driving forces, and structural aspects. Also, the most common analytical techniques used to gather deep insight into the aspects of CDs complexes are discussed and the perspectives for the surfactant-cyclodextrin complexes are pointed out.
Collapse
Affiliation(s)
- Larissa Dos Santos Silva Araújo
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Viale delle Scienze pad 17, 90128 Palermo, Italy; Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France
| | - Giuseppe Lazzara
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Viale delle Scienze pad 17, 90128 Palermo, Italy.
| | - Leonardo Chiappisi
- Institut Max von Laue - Paul Langevin, 71 avenue des Martyrs, 38042 Grenoble, France.
| |
Collapse
|
17
|
Thermodynamics of amyloid fibril formation from non-equilibrium experiments of growth and dissociation. Biophys Chem 2021; 271:106549. [PMID: 33578107 DOI: 10.1016/j.bpc.2021.106549] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Amyloid fibrils are ordered, non-covalent polymers of proteins that are linked to a range of diseases, as well as biological functions. Amyloid fibrils are often considered thermodynamically so stable that they appear to be irreversible, explaining why very few quantitative thermodynamic studies have been performed on amyloid fibrils, compared to the very large body of kinetic studies. Here we explore the thermodynamics of amyloid fibril formation by the protein PI3K-SH3, which forms amyloid fibrils under acidic conditions. We use quartz crystal microbalance (QCM) and develop novel temperature perturbation experiments based on differential scanning fluorimetry (DSF) to measure the temperature dependence of the fibril growth and dissociation rates, allowing us to quantitatively describe the thermodynamic stability of PI3K-SH3 amyloid fibrils between 10 and 75°C.
Collapse
|
18
|
Unveiling the Thermodynamic Aspects of Drug-Cyclodextrin Interactions Through Isothermal Titration Calorimetry. Methods Mol Biol 2020. [PMID: 33113137 DOI: 10.1007/978-1-0716-0920-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Due to their low toxicity and high aqueous solubility, cyclodextrins have emerged as a distinctive class of supramolecules with wide application in the pharmaceutical and food industry. Their ability to improve the water solubility, stability and pharmacokinetic profile of small molecules has established them as a rich toolkit for drug formulation. In order to improve the physicochemical characteristics and the pharmacokinetic profile of a drug through cyclodextrin inclusion, the proper cyclodextrin type has to be selected among the existing great variety consisting of both natural and synthetic variants. The selection of the most proper cyclodextrin variant comes after drug-cyclodextrin screening studies targeting the characterization of the complex formation and evaluation of the affinity and interaction forces participating in the complexation. Numerous analytical, spectroscopic, separation and electrochemical techniques have been applied to elucidate the interaction profile in a cyclodextrin-drug complex. Herein, we describe the application of Isothermal Titration Calorimetry (ITC) on cyclodextrin-drug complexes that enables the charting of the binding affinity and the thermodynamic profile of the inclusion complexes. We focus on the experimental design and present technical tips of the ITC application. To better illustrate the technique's rationale, the interaction between 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) and the antihypertensive drug losartan is investigated.
Collapse
|
19
|
Hornok V, Juhász Á, Paragi G, Kovács AN, Csapó E. Thermodynamic and kinetic insights into the interaction of kynurenic acid with human serum albumin: Spectroscopic and calorimetric approaches. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112869] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
20
|
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Comput Biol 2020; 16:e1007767. [PMID: 32365068 PMCID: PMC7282669 DOI: 10.1371/journal.pcbi.1007767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 03/02/2020] [Indexed: 11/19/2022] Open
Abstract
Many proteins have the potential to aggregate into amyloid fibrils, protein polymers associated with a wide range of human disorders such as Alzheimer’s and Parkinson’s disease. The thermodynamic stability of amyloid fibrils, in contrast to that of folded proteins, is not well understood: the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using a combination of theory, in vitro experiments, simulations of a coarse-grained protein model and meta-data analysis, we delineate the enthalpic and entropic contributions that dominate amyloid fibril elongation. Our prediction of a characteristic temperature-dependent enthalpic signature is confirmed by the performed calorimetric experiments and a meta-analysis over published data. From these results we are able to define the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability. Most proteins fold in the cell into stable, compact structures. Nevertheless, many proteins also have the ability to stick together, forming long fibrillar structures that are associated with a wide range of human disorders including Alzheimer’s and Parkinson’s disease. The exact nature of the amyloid-causing stickiness is not well understood, nevertheless amyloid fibrils show some very specific thermodynamic characteristics. Some fibrils even destabilise at low temperatures. In this work we translate hydrophobic theory previously used to model protein folding to fibril formation. We combine this theory with experimental measurements, simulations and meta-data analysis of different types of fibrils. This allowed us to unravel the nature of the stickiness in amyloid fibrils by observing the effect of temperature changes, specifically at low temperatures, on hydrophobicity.
Collapse
|
21
|
Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D. Tuning Allostery through Integration of Disorder to Order with a Residue Network. Biochemistry 2020; 59:790-801. [PMID: 31899864 DOI: 10.1021/acs.biochem.9b01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In allostery, a signal from one site in a protein is transmitted to a second site to alter its function. Due to its ubiquity in biology and the potential for its exploitation in drug and protein design, the molecular basis of allosteric communication continues to be the subject of intense research. Although allosterically coupled sites are frequently characterized by disorder, how communication between disordered segments occurs remains obscure. Allosteric activation of Escherichia coli BirA dimerization occurs via coupled distant disorder-to-order transitions. In this work, combined structural and computational studies reveal an extensive residue network in BirA. Substitution of several network residues yields large perturbations to allostery. Force distribution analysis reveals that disruptions to the disorder-to-order transitions through amino acid substitution are manifested in shifts in the energy experienced by network residues as well as alterations in packing of an α-helix that plays a critical role in allostery. The combined results reveal a highly distributed allosteric mechanism that is robust to sequence change.
Collapse
Affiliation(s)
- Jingheng Wang
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Riya Samanta
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Gregory Custer
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Christopher Look
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| |
Collapse
|
22
|
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations. J Comput Aided Mol Des 2020; 34:589-600. [PMID: 31974852 DOI: 10.1007/s10822-020-00294-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/17/2020] [Indexed: 10/25/2022]
Abstract
Host-guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host-guest systems in the SAMPL6 challenge. By biasing the spherical coordinates describing the relative position of the host and the guest, the initial-configuration-induced bias vanishes and all possible binding poses are explored. The agreement between the predictions and the experimental results and the observation of new binding poses indicate that the volume-based technique serves as a nice candidate for the calculation of binding free energies and the search of the binding poses.
Collapse
|
23
|
Hipólito-Nájera AR, Rodríguez-Laguna N, Reyes-García LI, Gómez-Vidales V, Rojas-Hernández A, Gómez-Balderas R, Moya-Hernández R. Thermodynamics of inclusion within cyclodextrins and structural evidence of Cu(indomethacin) 2 and Zn(indomethacin) 2 complexes in aqueous solutions. NEW J CHEM 2020. [DOI: 10.1039/d0nj03335a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cu(IMC)2 and Zn(IMC)2 inclusion within cyclodextrins is spontaneous, the former driven by entropic and the last by enthalpic contributions.
Collapse
Affiliation(s)
- Adrián Ricardo Hipólito-Nájera
- Laboratorio de Fisicoquímica Analítica
- Unidad de Investigación Multidisciplinaria
- Facultad de Estudios Superiores Cuautitlán
- Universidad Nacional Autónoma de México
- Cuautitlán Izcalli
| | - Norma Rodríguez-Laguna
- Laboratorio de Fisicoquímica Analítica
- Unidad de Investigación Multidisciplinaria
- Facultad de Estudios Superiores Cuautitlán
- Universidad Nacional Autónoma de México
- Cuautitlán Izcalli
| | - Luis I. Reyes-García
- Laboratorio de Fisicoquímica Analítica
- Unidad de Investigación Multidisciplinaria
- Facultad de Estudios Superiores Cuautitlán
- Universidad Nacional Autónoma de México
- Cuautitlán Izcalli
| | - Virginia Gómez-Vidales
- Instituto de Química
- Universidad Nacional Autónoma de México
- Circuito exterior
- Ciudad Universitaria
- 04510 Coyoacán
| | | | - Rodolfo Gómez-Balderas
- Laboratorio de Fisicoquímica Analítica
- Unidad de Investigación Multidisciplinaria
- Facultad de Estudios Superiores Cuautitlán
- Universidad Nacional Autónoma de México
- Cuautitlán Izcalli
| | - Rosario Moya-Hernández
- Laboratorio de Fisicoquímica Analítica
- Unidad de Investigación Multidisciplinaria
- Facultad de Estudios Superiores Cuautitlán
- Universidad Nacional Autónoma de México
- Cuautitlán Izcalli
| |
Collapse
|
24
|
Sun Z, Wang X, Zhang JZH. Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding. Phys Chem Chem Phys 2019; 22:1511-1524. [PMID: 31872826 DOI: 10.1039/c9cp05980f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The transcriptional regulator TtgR belongs to the TetR family of transcriptional repressors. It depresses the transcription of the TtgABC operon and itself and thus regulates the extrusion of noxious chemicals with efflux pumps in bacterial cells. As the ligand-binding domain of TtgR is rather flexible, it can bind with a number of structurally diverse ligands, such as antibiotics, flavonoids and aromatic solvents. In the current work, we perform equilibrium and nonequilibrium alchemical free energy simulation to predict the binding affinities of a series of ligands targeting the TtgR protein and an agreement between the theoretical prediction and the experimental result is observed. End-point methods MM/PBSA and MM/GBSA are also employed for comparison. We further study the interaction maps and contacts between the protein and the ligand and identify important interactions in the protein-ligand binding cases. The dynamics fluctuation and secondary structures are also investigated. The current work sheds light on atomic and thermodynamic understanding of the TtgR-ligand interactions.
Collapse
Affiliation(s)
- Zhaoxi Sun
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany. and State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and Institute of Computational Science, Università della Svizzera italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China and Department of Chemistry, New York University, NY, NY 10003, USA.
| |
Collapse
|
25
|
Niether D, Wiegand S. Thermophoresis of biological and biocompatible compounds in aqueous solution. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:503003. [PMID: 31491783 DOI: 10.1088/1361-648x/ab421c] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.
Collapse
Affiliation(s)
- D Niether
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | | |
Collapse
|
26
|
Schönbeck C, Holm R. Exploring the Origins of Enthalpy–Entropy Compensation by Calorimetric Studies of Cyclodextrin Complexes. J Phys Chem B 2019; 123:6686-6693. [DOI: 10.1021/acs.jpcb.9b03393] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Christian Schönbeck
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
| | - René Holm
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark
- Drug Product Development, Janssen Research and Development, Johnson & Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| |
Collapse
|
27
|
Khrapunov S. The Enthalpy-entropy Compensation Phenomenon. Limitations for the Use of Some Basic Thermodynamic Equations. Curr Protein Pept Sci 2019; 19:1088-1091. [PMID: 29779476 DOI: 10.2174/1389203719666180521092615] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/10/2018] [Accepted: 05/16/2018] [Indexed: 11/22/2022]
Abstract
The thermodynamic analyses of proteins, protein-ligands and protein-nucleic acid complexes involves the entropy-enthalpy (S-H) compensation phenomenon. We have examined the question whether the observed compensation is artificial or reflects anything more than the well-known laws of statistical thermodynamics (so-called extra-thermodynamic compensation). We have shown that enthalpy- entropy compensation (EEC) is mainly the trivial consequence of the basic thermodynamic laws and there are no experimental evidences for existence of the extra-thermodynamic compensation. In most cases EEC obtained in the experiments through the plot enthalpies (ΔH) and entropies (TΔS) versus one another is meaningless due to the large correlated errors in ΔH and TΔS, unless special measures are taken to minimize, quantify and propagate these errors. Van't Hoff equation can be used for entropy calculation in limited cases when enthalpy is measured in independent experiments. Eyring equation cannot be used for calculation of entropy in any case and should be excluded from scientific use. Both equation, Van't Hoff and Eyring cannot be used for simultaneous calculation of the enthalpy and entropy values using one set of data. All the data obtained in this way should be recognized as erroneous.
Collapse
Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, United States
| |
Collapse
|
28
|
Gao S, Holkar A, Srivastava S. Protein-Polyelectrolyte Complexes and Micellar Assemblies. Polymers (Basel) 2019; 11:E1097. [PMID: 31261765 PMCID: PMC6680422 DOI: 10.3390/polym11071097] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
In this review, we highlight the recent progress in our understanding of the structure, properties and applications of protein-polyelectrolyte complexes in both bulk and micellar assemblies. Protein-polyelectrolyte complexes form the basis of the genetic code, enable facile protein purification, and have emerged as enterprising candidates for simulating protocellular environments and as efficient enzymatic bioreactors. Such complexes undergo self-assembly in bulk due to a combined influence of electrostatic interactions and entropy gains from counterion release. Diversifying the self-assembly by incorporation of block polyelectrolytes has further enabled fabrication of protein-polyelectrolyte complex micelles that are multifunctional carriers for therapeutic targeted delivery of proteins such as enzymes and antibodies. We discuss research efforts focused on the structure, properties and applications of protein-polyelectrolyte complexes in both bulk and micellar assemblies, along with the influences of amphoteric nature of proteins accompanying patchy distribution of charges leading to unique phenomena including multiple complexation windows and complexation on the wrong side of the isoelectric point.
Collapse
Affiliation(s)
- Shang Gao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Advait Holkar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Samanvaya Srivastava
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
29
|
Sung HL, Nesbitt DJ. Novel Heat-Promoted Folding Dynamics of the yybP-ykoY Manganese Riboswitch: Kinetic and Thermodynamic Studies at the Single-Molecule Level. J Phys Chem B 2019; 123:5412-5422. [DOI: 10.1021/acs.jpcb.9b02852] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | - David J. Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States
| |
Collapse
|
30
|
General method for kinetic and thermodynamic evaluation of a receptor model peptide-drug molecule interaction studied by surface plasmon resonance. Microchem J 2019. [DOI: 10.1016/j.microc.2019.03.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
31
|
Terdale SS, Warke IJ. Thermodynamic studies of phosphonium and imidazolium based ionic liquids in water at 298.15 K: Application of McMillan-Mayer theory and Pitzer model. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
32
|
Sun Z, Wang X, Zhang JZ. Determination of binding affinities of 3-Hydroxy-3-Methylglutaryl Coenzyme A reductase inhibitors from free energy calculation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
33
|
Wang X, Sun Z. Understanding PIM-1 kinase inhibitor interactions with free energy simulation. Phys Chem Chem Phys 2019; 21:7544-7558. [PMID: 30895980 DOI: 10.1039/c9cp00070d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The proviral integration site of the Moloney leukemia virus (PIM) family includes three homologous members. PIM-1 kinase is an important target in effective therapeutic interventions of lymphomas, prostate cancer and leukemia. In the current work, we performed free energy calculations to calculate the binding affinities of several inhibitors targeting this protein. The alchemical method with integration and perturbation-based estimators and the end-point methods were compared. The computational results indicated that the alchemical method can accurately predict the binding affinities, while the end-point methods give relatively unreliable predictions. Decomposing the free energy difference into enthalpic and entropic components with MBAR reweighting enabled us to investigate the detailed thermodynamic parameters with which the entropy-enthalpy compensation in this protein-ligand binding case is identified. We then studied the conformational ensemble, and the important protein-ligand interactions were identified. The current work sheds light on the understanding of the PIM-1-kinase-inhibitor interactions at the atomic level and will be useful in the further development of potential drugs.
Collapse
Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | | |
Collapse
|
34
|
Boden S, Reise F, Kania J, Lindhorst TK, Hartmann L. Sequence-Defined Introduction of Hydrophobic Motifs and Effects in Lectin Binding of Precision Glycomacromolecules. Macromol Biosci 2019; 19:e1800425. [PMID: 30707496 DOI: 10.1002/mabi.201800425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/11/2019] [Indexed: 12/11/2022]
Abstract
This study investigates the influence of an increasingly hydrophobic backbone of multivalent glycomimetics based on sequence-defined oligo(amidoamines) on their resulting affinity toward bacterial lectins. Glycomacromolecules are obtained by stepwise assembly of tailor-made building blocks on solid support, using both hydrophobic aliphatic and aromatic building blocks to enable a gradual change in hydrophobicity of the backbone. Their binding behavior toward model lectin Concanavalin A (ConA) is evaluated using isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) showing higher affinities for glycomacromolecules with higher content of hydrophobic and aromatic moieties in the backbone. Finally, glycomacromolecules are tested in a bacterial adhesion inhibition study against Escherichia coli where more hydrophobic backbones yield higher inhibitory potentials most likely due to additional secondary interactions with hydrophobic regions of the protein receptor as well as a change in conformation exposing carbohydrate ligands for increased binding. Overall, the results highlight the influence and thereby importance of the polymer backbone itself on the resulting properties of polymeric biomimetics.
Collapse
Affiliation(s)
- Sophia Boden
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Franziska Reise
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3-4, 24118, Kiel, Germany
| | - Jessica Kania
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thisbe K Lindhorst
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3-4, 24118, Kiel, Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| |
Collapse
|
35
|
Jharimune S, Sathe AA, Rioux RM. Thermochemical Measurements of Cation Exchange in CdSe Nanocrystals Using Isothermal Titration Calorimetry. NANO LETTERS 2018; 18:6795-6803. [PMID: 30160126 DOI: 10.1021/acs.nanolett.8b02661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Among the various reported post synthetic modifications of colloidal nanocrystals, cation exchange (CE) is one of the most promising and versatile approaches for the synthesis of nanostructures that cannot be directly synthesized from their constitutive precursors. Numerous studies have reported on the qualitative analysis of these reactions, but rigorous quantitative study of the thermodynamics of CE in colloidal nanoparticles is still lacking. We demonstrate using isothermal titration calorimetry (ITC), the thermodynamics of the CE between cadmium selenide (CdSe) nanocrystals and silver in solution can be quantified. We survey the influence of CdSe nanocrystal diameter, capping ligands and temperature on the thermodynamics of the exchange reaction. Results obtained from ITC provide a detailed description of overall thermodynamic parameters-equilibrium constant ( K eq), enthalpy (Δ H), entropy (Δ S) and stoichiometry ( n)-of the exchange reaction. We compared the free energy change of reaction (Δ G) between CdSe and Ag+ obtained directly from ITC for both CdSe bulk and nanoparticles with values calculated from previously reported methods. While the calculated value is closer to the experimentally obtained Δ G rxn for bulk particles, nanocrystals show an additional Gibbs free energy stabilization of ∼-14 kJ/mol Se. We discuss a thermochemical cycle elucidating the steps involved in the overall cation exchange process. This work demonstrates the application of ITC to probe the thermochemistry of nanoscale transformations under relevant solution conditions.
Collapse
|
36
|
Parikh V, Gupta P. Thermodynamic analysis of r-hGH-polymer surface Interaction using isothermal titration calorimetry. Growth Horm IGF Res 2018; 42-43:86-93. [PMID: 30368133 DOI: 10.1016/j.ghir.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 11/25/2022]
Abstract
Delivery of protein drugs would be an effective approach if mechanistic understanding of protein adsorption at solid/liquid surface is obtained and nonspecific adsorption can be controlled. This study involves evaluation of the thermodynamic parameters for interaction between recombinant human growth hormone (r-hGH) and nanoparticles of poly (lactic- co- glycolic) acid polymer of different molecular weight. Energy changes related to protein-nanoparticle interactions are usually very small and isothermal titration calorimetry (ITC) is the only technique that determines the binding constant (Ka), enthalpy, (ΔH) and stoichiometry, (n) in a single experiment. Therefore, we used ITC to study the energetics of the binding of r-hGH with PLGA nanoparticles. The largely negative ∆H and ∆S suggested that binding was driven by non-classical hydrophobic effect for interaction with PLGA 50501A and PLGA 8515E nanoparticles at pH 7.2 where higher surface coverage was noted for the latter. Endothermic, entropically driven reaction was observed upon interaction of r-hGH with PLGA 5050 5E nanoparticles at pH 7.2, PLGA 5050 1A nanoparticles at pH 5.3 and pH 4.0. Moreover, negative value of ΔCp for PLGA 50501A NPs at pH 7.2 indicated cooperative disorder of hydrogen-bonding networks and no evidence of hydrophobic elements. ITC proved to be very efficient method in studying the thermodynamics of the protein polymer interaction. In agreement with results from previous studies using fluorescence spectroscopy, circular dichroism and dynamic light scattering in our laboratory, this study demonstrated that adsorption can be controlled by selecting the polymer of low to moderate hydrophobicity depending on the pH of media.
Collapse
Affiliation(s)
- Vaishnavi Parikh
- Department of pharmaceutics, University of the Sciences, Philadelphia, PA, USA.
| | - Pardeep Gupta
- Department of pharmaceutics, University of the Sciences, Philadelphia, PA, USA
| |
Collapse
|
37
|
Ran Q, Xu X, Dzubiella J, Haag R, Ballauff M. Thermodynamics of the Binding of Lysozyme to a Dendritic Polyelectrolyte: Electrostatics Versus Hydration. ACS OMEGA 2018; 3:9086-9095. [PMID: 31459043 PMCID: PMC6644519 DOI: 10.1021/acsomega.8b01493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/30/2018] [Indexed: 05/25/2023]
Abstract
The interaction between dendritic polyglycerol sulfate (dPGS) of the second generation and lysozyme was studied by isothermal titration calorimetry (ITC) at different temperatures and salt concentrations. Analysis by ITC showed that 2-3 lysozyme molecules were bound to each dPGS. The resulting binding constant K b and the Gibbs free energy ΔG o decreased markedly with increasing salt concentration but were nearly independent of temperature. The salt dependence of K b led to the conclusion that ca. 3 counterions bound to dPGS were released upon complex formation. The gain in entropy ΔG ci by this counterion-release scales logarithmically with salt concentration and is the main driving force for binding. The temperature dependence of ΔG o was analyzed by the nonlinear van't Hoff plot, taking into account a finite heat capacity change ΔC p,vH. This evaluation led to the binding enthalpy ΔH vH and the binding entropy ΔS vH. Both quantities varied strongly with temperature and even changed sign, but they compensated each other throughout the entire range of temperature. Coarse-grained computer simulations with explicit salt and implicit water were used to obtain the binding free energies that agreed with ITC results. Thus, electrostatic factors were the driving forces for binding whereas all hydration contributions leading to the strongly varying ΔH vH and ΔS vH canceled out. The calorimetric enthalpy ΔH ITC measured directly by ITC differed largely from ΔH vH. ITC measurements done in two buffer systems with different ionization enthalpies revealed that binding was linked to buffer ionization and a partial protonation of the protein.
Collapse
Affiliation(s)
- Qidi Ran
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Takustr. 3, 14195 Berlin, Germany
- Institute
of Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
- Multifunctional
Biomaterials for Medicine, Helmholtz Virtual Institute, Kantstr. 55, 14513 Teltow-Seehof, Germany
| | - Xiao Xu
- School
of Chemical Engineering, Nanjing University
of Science and Technology, 200 Xiao Ling Wei, 210094 Nanjing, P. R. China
| | - Joachim Dzubiella
- Institute
of Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
- Multifunctional
Biomaterials for Medicine, Helmholtz Virtual Institute, Kantstr. 55, 14513 Teltow-Seehof, Germany
- Physikalisches
Institut, Albert-Ludwigs-Universität, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Rainer Haag
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Takustr. 3, 14195 Berlin, Germany
- Multifunctional
Biomaterials for Medicine, Helmholtz Virtual Institute, Kantstr. 55, 14513 Teltow-Seehof, Germany
| | - Matthias Ballauff
- Institute
of Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
- Multifunctional
Biomaterials for Medicine, Helmholtz Virtual Institute, Kantstr. 55, 14513 Teltow-Seehof, Germany
- Institut
für Physik, Humboldt-Universität
zu Berlin, Newtonstr. 15, 12489 Berlin, Germany
| |
Collapse
|
38
|
Beerens K, Mazurenko S, Kunka A, Marques SM, Hansen N, Musil M, Chaloupkova R, Waterman J, Brezovsky J, Bednar D, Prokop Z, Damborsky J. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Sergio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| |
Collapse
|
39
|
Meekrathok P, Stubbs KA, Suginta W. Potent inhibition of a GH20 exo-β-N-acetylglucosaminidase from marine Vibrio bacteria by reaction intermediate analogues. Int J Biol Macromol 2018; 115:1165-1173. [DOI: 10.1016/j.ijbiomac.2018.04.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/14/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
|
40
|
Fox JM, Zhao M, Fink MJ, Kang K, Whitesides GM. The Molecular Origin of Enthalpy/Entropy Compensation in Biomolecular Recognition. Annu Rev Biophys 2018; 47:223-250. [DOI: 10.1146/annurev-biophys-070816-033743] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon—termed enthalpy/entropy (H/S) compensation—hinders efforts in biomolecular design, and its incidence—often a surprise to experimentalists—makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins. Studying H/S compensation can help illuminate the still-murky roles of water and dynamics in biomolecular recognition and self-assembly. This review summarizes known sources of H/ S compensation (real and perceived) and lays out a conceptual framework for understanding and dissecting—and, perhaps, avoiding or exploiting—this phenomenon in biophysical systems.
Collapse
Affiliation(s)
- Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
| | - Mengxia Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Michael J. Fink
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, Republic of Korea
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
- The Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
41
|
Stabilizers influence drug-polymer interactions and physicochemical properties of disulfiram-loaded poly-lactide-co-glycolide nanoparticles. Future Sci OA 2017; 4:FSO263. [PMID: 29379637 PMCID: PMC5778387 DOI: 10.4155/fsoa-2017-0091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/06/2017] [Indexed: 12/04/2022] Open
Abstract
Aim: Stabilizers are known to be an integral component of polymeric nanostructures. Ideally, they manipulate physicochemical properties of nanoparticles. Based on this hypothesis, we demonstrated that disulfiram (drug) and Poly-lactide-co-glycolide (polymer) interactions and physicochemical properties of their nanoparticles formulations are significantly influenced by the choice of stabilizers. Methodology: Electron microscopy, differential scanning calorimetry, x-ray diffraction, Raman spectrum analysis, isothermal titration calorimetry and in silico docking studies were performed. Results & discussion: Polysorbate 80 imparted highest crystallinity while Triton-X 100 imparted highest rigidity, possibly influencing drug bioavailability, blood-retention time, cellular uptake and sustained drug release. All the molecular interactions were hydrophobic in nature and entropy driven. Therefore, polymeric nanoparticles may be critically manipulated to streamline the passive targeting of drug-loaded nanoparticles. Polymeric nanoparticles are futuristic drug-delivering platforms that have many potential advantages above conventional drug-delivery tools. They are mainly composed of a polymer, stabilizer and the therapeutic ingredient. A number of researches are on-going to improvise various characteristics of polymeric nanoparticles, in order to enhance its efficacy. The current study is one such domain where we emphasize on identifying potential stabilizing factors that are involved in nanoparticles formation and their drug entrapment and release properties.
Collapse
|
42
|
Cornish-Bowden A. Enthalpy–entropy compensation and the isokinetic temperature in enzyme catalysis. J Biosci 2017; 42:665-670. [DOI: 10.1007/s12038-017-9719-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
43
|
Samatanga B, Cléry A, Barraud P, Allain FHT, Jelesarov I. Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs. Nucleic Acids Res 2017; 45:6037-6050. [PMID: 28334819 PMCID: PMC5449602 DOI: 10.1093/nar/gkx136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 02/16/2017] [Indexed: 01/05/2023] Open
Abstract
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM–ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process.
Collapse
Affiliation(s)
- Brighton Samatanga
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland.,Department of Biochemistry, University of Zürich, Wintherthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, CH-8093 Zurich, Switzerland
| | - Ilian Jelesarov
- Department of Biochemistry, University of Zürich, Wintherthurerstrasse 190, CH-8057 Zurich, Switzerland
| |
Collapse
|
44
|
Wild J, Meier TNG, Pöllath S, Kronseder M, Bauer A, Chacon A, Halder M, Schowalter M, Rosenauer A, Zweck J, Müller J, Rosch A, Pfleiderer C, Back CH. Entropy-limited topological protection of skyrmions. SCIENCE ADVANCES 2017; 3:e1701704. [PMID: 28975152 PMCID: PMC5621974 DOI: 10.1126/sciadv.1701704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/07/2017] [Indexed: 05/27/2023]
Abstract
Magnetic skyrmions are topologically protected whirls that decay through singular magnetic configurations known as Bloch points. We used Lorentz transmission electron microscopy to infer the energetics associated with the topological decay of magnetic skyrmions far from equilibrium in the chiral magnet Fe1-x Co x Si. We observed that the lifetime τ of the skyrmions depends exponentially on temperature, [Formula: see text]. The prefactor τ0 of this Arrhenius law changes by more than 30 orders of magnitude for small changes of the magnetic field, reflecting a substantial reduction of the lifetime of skyrmions by entropic effects and, thus, an extreme case of enthalpy-entropy compensation. Such compensation effects, being well known across many different scientific disciplines, affect topological transitions and, thus, topological protection on an unprecedented level.
Collapse
Affiliation(s)
- Johannes Wild
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| | - Thomas N. G. Meier
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| | - Simon Pöllath
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| | - Matthias Kronseder
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| | - Andreas Bauer
- Physik Department, Technische Universität Bremen, D-85748 Garching, Germany
| | - Alfonso Chacon
- Physik Department, Technische Universität Bremen, D-85748 Garching, Germany
| | - Marco Halder
- Physik Department, Technische Universität Bremen, D-85748 Garching, Germany
| | - Marco Schowalter
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, D-28359 Bremen, Germany
| | - Andreas Rosenauer
- Institut für Festkörperphysik, Universität Bremen, Otto-Hahn-Allee 1, D-28359 Bremen, Germany
| | - Josef Zweck
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| | - Jan Müller
- Institut für Theoretische Physik, Universität zu Köln, D-50937 Köln, Germany
| | - Achim Rosch
- Institut für Theoretische Physik, Universität zu Köln, D-50937 Köln, Germany
| | | | - Christian H. Back
- Institut für Experimentelle Physik, Universität Regensburg, D-93040 Regensburg, Germany
| |
Collapse
|
45
|
Niether D, Kawaguchi T, Hovancová J, Eguchi K, Dhont JKG, Kita R, Wiegand S. Role of Hydrogen Bonding of Cyclodextrin-Drug Complexes Probed by Thermodiffusion. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8483-8492. [PMID: 28780866 DOI: 10.1021/acs.langmuir.7b02313] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Temperature gradient-induced migration of biomolecules, known as thermophoresis or thermodiffusion, changes upon ligand binding. In recent years, this effect has been used to determine protein-ligand binding constants. The mechanism through which thermodiffusive properties change when complexes are formed, however, is not understood. An important contribution to thermodiffusive properties originates from the thermal response of hydrogen bonds. Because there is a considerable difference between the degree of solvation of the protein-ligand complex and its isolated components, ligand-binding is accompanied by a significant change in hydration. The aim of the present work is therefore to investigate the role played by hydrogen bonding on the change in thermodiffusive behavior upon ligand-binding. As a model system, we use cyclodextrins (CDs) and acetylsalicylic acid (ASA), where quite a significant change in hydration is expected and where no conformational changes occur when a CD/ASA complex is formed in aqueous solution. Thermophoresis was investigated in the temperature range of 10-50 °C by infrared thermal diffusion forced Rayleigh scattering. Nuclear magnetic resonance measurements were performed at 25 °C to obtain information about the structure of the complexes. All CD/ASA complexes show a stronger affinity toward regions of lower temperature compared to the free CDs. We found that the temperature sensitivity of thermophoresis correlates with the 1-octanol/water partition coefficient. This observation not only establishes the relation between thermodiffusion and degree of hydrogen bonding but also opens the possibility to relate thermodiffusive properties of complexes to their partition coefficient, which cannot be determined otherwise. This concept is especially interesting for protein-ligand complexes where the protein undergoes a conformational change, different from the CD/ASA complexes, giving rise to additional changes in their hydrophilicity.
Collapse
Affiliation(s)
- Doreen Niether
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH , D-52428 Jülich, Germany
| | | | - Jana Hovancová
- Chemistry Department, Pavol Jozef Šafárik Univerzity , 041 80 Košice, Slovakia
| | | | - Jan K G Dhont
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH , D-52428 Jülich, Germany
- Department of Physics, Heinrich-Heine-Universität Düsseldorf , D-40225 Düsseldorf, Germany
| | | | - Simone Wiegand
- ICS-3 Soft Condensed Matter, Forschungszentrum Jülich GmbH , D-52428 Jülich, Germany
- Department für Chemie-Physikalische Chemie, Universität zu Köln , D-50939 Cologne, Germany
| |
Collapse
|
46
|
Khan AY, Suresh Kumar G. Exploring the binding interaction of potent anticancer drug topotecan with human serum albumin: spectroscopic, calorimetric and fibrillation study. J Biomol Struct Dyn 2017; 36:2463-2473. [DOI: 10.1080/07391102.2017.1359671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| |
Collapse
|
47
|
Idili A, Ricci F, Vallée-Bélisle A. Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves. Nucleic Acids Res 2017; 45:7571-7580. [PMID: 28605461 PMCID: PMC5737623 DOI: 10.1093/nar/gkx498] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/13/2022] Open
Abstract
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
Collapse
Affiliation(s)
- Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Montreal, Québec H3T-1J4, Canada
| |
Collapse
|
48
|
Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
Collapse
Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| |
Collapse
|
49
|
Harish B, Swapna GVT, Kornhaber GJ, Montelione GT, Carey J. Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR. Proteins 2017; 85:731-740. [PMID: 28120439 DOI: 10.1002/prot.25252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 12/20/2016] [Accepted: 01/04/2017] [Indexed: 11/11/2022]
Abstract
The nature of flexibility in the helix-turn-helix region of E. coli trp aporepressor has been unexplained for many years. The original ensemble of nuclear magnetic resonance (NMR structures showed apparent disorder, but chemical shift and relaxation measurements indicated a helical region. Nuclear Overhauser effect (NOE) data for a temperature-sensitive mutant showed more helical character in its helix-turn-helix region, but nevertheless also led to an apparently disordered ensemble. However, conventional NMR structure determination methods require all structures in the ensemble to be consistent with every NOE simultaneously. This work uses an alternative approach in which some structures of the ensemble are allowed to violate some NOEs to permit modeling of multiple conformational states that are in dynamic equilibrium. Newly measured NOE data for wild-type aporepressor are used as time-averaged distance restraints in molecular dynamics simulations to generate an ensemble of helical conformations that is more consistent with the observed NMR data than the apparent disorder in the previously reported NMR structures. The results indicate the presence of alternating helical conformations that provide a better explanation for the flexibility of the helix-turn-helix region of trp aporepressor. Structures representing these conformations have been deposited with PDB ID: 5TM0. Proteins 2017; 85:731-740. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
| | - G V T Swapna
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Gregory J Kornhaber
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, New Jersey, 08544
| |
Collapse
|
50
|
Hamre AG, Frøberg EE, Eijsink VGH, Sørlie M. Thermodynamics of tunnel formation upon substrate binding in a processive glycoside hydrolase. Arch Biochem Biophys 2017; 620:35-42. [PMID: 28359644 DOI: 10.1016/j.abb.2017.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 11/18/2022]
Abstract
Glycoside hydrolases (GHs) catalyze the hydrolysis of glycosidic bonds and are key enzymes in carbohydrate metabolism. Efficient degradation of recalcitrant polysaccharides such as chitin and cellulose is accomplished due to synergistic enzyme cocktails consisting of accessory enzymes and mixtures of GHs with different modes of action and active site topologies. The substrate binding sites of chitinases and cellulases often have surface exposed aromatic amino acids and a tunnel or cleft topology. The active site of the exo-processive chitinase B (ChiB) from Serratia marcescens is partially closed, creating a tunnel-like catalytic cleft. To gain insight in the fundamental principles of substrate binding in this enzyme, we have studied the contribution of five key residues involved in substrate binding and tunnel formation to the thermodynamics of substrate binding. Mutation of Trp97, Phe190, Trp220 and Glu221, which are all part of the tunnel walls, resulted in significant less favorable conformational entropy change (ΔS°conf) upon binding (-TΔΔS°conf = ∼5 kcal/mol). This suggest that these residues are important for the structural rigidity and pre-shaping of the tunnel prior to binding. Mutation of Asp316, which, by forming a hydrogen bond to Trp97 is crucial in the active-site tunnel roof, resulted in a more favorable ΔS°conf relative to the wild type (-TΔΔS°conf = -2.2 kcal/mol). This shows that closing the tunnel-roof comes with an entropy cost, as previously suggested based on the crystal structures of GHs with tunnel topologies in complex with their substrates.
Collapse
Affiliation(s)
- Anne Grethe Hamre
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Emil Ebbestad Frøberg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway
| | - Morten Sørlie
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO 5003, N-1432 Ås, Norway.
| |
Collapse
|