1
|
Broz M, Oostenbrink C, Bren U. The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J Chem Inf Model 2024; 64:2077-2083. [PMID: 38477115 DOI: 10.1021/acs.jcim.3c01937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The impact of microwave (MW) irradiation on protein folding, potentially inciting misfolding, was investigated by employing molecular dynamics (MD) simulations. Twenty-nine proteins were subjected to MD simulations under equilibrium (300 K) and MW conditions, where the rotational temperature was elevated to 700 K. The utilized replacement model captures the microwave effects of δ- and γ-relaxation processes (frequency range of ∼300 MHz to ∼20 GHz). The results disclosed that MW heating incited a shift toward more compact protein conformations, as indicated by decreased root-mean-square deviations, root-mean-square fluctuations, head-to-tail distances, and radii of gyration. This compaction was attributed to the intensification of intramolecular electrostatic interactions and hydrogen bonds within the protein caused by MW-destabilized hydrogen bonds between the protein and solvent. The solvent-accessible surface area (SASA), particularly that of polar amino-acid residues, shrank under MW conditions, corresponding to a reduced polarity of the water solvent. However, MW irradiation produced no significant alterations in protein secondary structures; hence, MW heating was observed to primarily affect the protein tertiary structures.
Collapse
Affiliation(s)
- Matic Broz
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, Maribor SI-2000, Slovenia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna 1190, Austria
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, Maribor SI-2000, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, Koper SI-6000, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
| |
Collapse
|
2
|
Sláma V, Perlík V, Langhals H, Walter A, Mančal T, Hauer J, Šanda F. Anharmonic Molecular Motion Drives Resonance Energy Transfer in peri-Arylene Dyads. Front Chem 2020; 8:579166. [PMID: 33330367 PMCID: PMC7732524 DOI: 10.3389/fchem.2020.579166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Spectral and dynamical properties of molecular donor-acceptor systems strongly depend on the steric arrangement of the constituents with exciton coupling J as a key control parameter. In the present work we study two peri-arylene based dyads with orthogonal and parallel transition dipoles for donor and acceptor moieties, respectively. We show that the anharmonic multi-well character of the orthogonal dyad's intramolecular potential explains findings from both stationary and time-resolved absorption experiments. While for a parallel dyad, standard quantum chemical estimates of J at 0 K are in good agreement with experimental observations, J becomes vanishingly small for the orthogonal dyad, in contrast to its ultrafast experimental transfer times. This discrepancy is not resolved even by accounting for harmonic fluctuations along normal coordinates. We resolve this problem by supplementing quantum chemical approaches with dynamical sampling of fluctuating geometries. In contrast to the moderate Gaussian fluctuations of J for the parallel dyad, fluctuations for the orthogonal dyad are found to follow non-Gaussian statistics leading to significantly higher effective J in good agreement with experimental observations. In effort to apply a unified framework for treating the dynamics of optical coherence and excitonic populations of both dyads, we employ a vibronic approach treating electronic and selected vibrational degrees on an equal footing. This vibronic model is used to model absorption and fluorescence spectra as well as donor-acceptor transport dynamics and covers the more traditional categories of Förster and Redfield transport as limiting cases.
Collapse
Affiliation(s)
- Vladislav Sláma
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Václav Perlík
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Heinz Langhals
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Walter
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomáš Mančal
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Jürgen Hauer
- Professur für Dynamische Spektroskopien, Fakultät für Chemie, Technische Universität München, Munich, Germany
| | - František Šanda
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| |
Collapse
|
3
|
Diem M, Oostenbrink C. The effect of different cutoff schemes in molecular simulations of proteins. J Comput Chem 2020; 41:2740-2749. [PMID: 33026106 PMCID: PMC7756334 DOI: 10.1002/jcc.26426] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 01/02/2023]
Abstract
Molecular simulations of nanoscale systems invariably involve assumptions and approximations to describe the electrostatic interactions, which are long‐ranged in nature. One approach is the use of cutoff schemes with a reaction‐field contribution to account for the medium outside the cutoff scheme. Recent reports show that macroscopic properties may depend on the exact choice of cutoff schemes in modern day simulations. In this work, a systematic analysis of the effects of different cutoff schemes was performed using a set of 52 proteins. We find no statistically significant differences between using a twin‐range or a single‐range cutoff scheme. Applying the cutoff based on charge groups or based on atomic positions, does lead to significant differences, which is traced to the cutoff noise for energies and forces. While group‐based cutoff schemes show increased cutoff noise in the potential energy, applying an atomistic cutoff leads to artificial structure in the solvent at the cutoff distance. Carefully setting the temperature control, or using an atomistic cutoff for the solute and a group‐based cutoff for the solvent significantly reduces the effects of the cutoff noise, without introducing structure in the solvent. This study aims to deepen the understanding of the implications different cutoffs have on molecular dynamics simulations.
Collapse
Affiliation(s)
- Matthias Diem
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
4
|
Affiliation(s)
- Leonard P. Heinz
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| |
Collapse
|
5
|
Jandova Z, Jespers W, Sotelo E, Gutiérrez-de-Terán H, Oostenbrink C. Free-Energy Calculations for Bioisosteric Modifications of A 3 Adenosine Receptor Antagonists. Int J Mol Sci 2019; 20:E3499. [PMID: 31315296 DOI: 10.3390/ijms20143499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 11/16/2022] Open
Abstract
Adenosine receptors are a family of G protein-coupled receptors with increased attention as drug targets on different indications. We investigate the thermodynamics of ligand binding to the A3 adenosine receptor subtype, focusing on a recently reported series of diarylacetamidopyridine inhibitors via molecular dynamics simulations. With a combined approach of thermodynamic integration and one-step perturbation, we characterize the impact of the charge distribution in a central heteroaromatic ring on the binding affinity prediction. Standard charge distributions according to the GROMOS force field yield values in good agreement with the experimental data and previous free energy calculations. Subsequently, we examine the thermodynamics of inhibitor binding in terms of the energetic and entropic contributions. The highest entropy penalties are found for inhibitors with methoxy substituents in meta position of the aryl groups. This bulky group restricts rotation of aromatic rings attached to the pyrimidine core which leads to two distinct poses of the ligand. Our predictions support the previously proposed binding pose for the o-methoxy ligand, yielding in this case a very good correlation with the experimentally measured affinities with deviations below 4 kJ/mol.
Collapse
|
6
|
Abstract
![]()
Single-point mutations
in proteins can greatly influence protein
stability, binding affinity, protein function or its expression per
se. Here, we present accurate and efficient predictions of the free
energy of mutation of amino acids. We divided the complete mutational
free energy into an uncharging step, which we approximate by a third-power
fitting (TPF) approach, and an annihilation step, which we approximate
using the one-step perturbation (OSP) method. As a diverse set of
test systems, we computed the solvation free energy of all amino acid
side chain analogues and obtained an excellent agreement with thermodynamic
integration (TI) data. Moreover, we calculated mutational free energies
in model tripeptides and established an efficient protocol involving
a single reference state. Again, the approximate methods agreed excellently
with the TI references, with a root-mean-square error of only 3.6
kJ/mol over 17 mutations. Our combined TPF+OSP approach does show
not only a very good agreement but also a 2-fold higher efficiency
than full blown TI calculations.
Collapse
Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Daniel Fast
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Martina Setz
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| |
Collapse
|
7
|
Jandova Z, Trosanova Z, Weisova V, Oostenbrink C, Hritz J. Free energy calculations on the stability of the 14-3-3ζ protein. Biochim Biophys Acta Proteins Proteom 2017; 1866:442-450. [PMID: 29203375 DOI: 10.1016/j.bbapap.2017.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/31/2017] [Accepted: 11/25/2017] [Indexed: 01/08/2023]
Abstract
Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
Collapse
Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Zuzana Trosanova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Veronika Weisova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Jozef Hritz
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic.
| |
Collapse
|
8
|
Nagy G, Oostenbrink C, Hritz J. Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. PLoS One 2017; 12:e0180633. [PMID: 28727767 PMCID: PMC5519036 DOI: 10.1371/journal.pone.0180633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 06/19/2017] [Indexed: 11/19/2022] Open
Abstract
The 14-3-3 protein family performs regulatory functions in eukaryotic organisms by binding to a large number of phosphorylated protein partners. Whilst the binding mode of the phosphopeptides within the primary 14-3-3 binding site is well established based on the crystal structures of their complexes, little is known about the binding process itself. We present a computational study of the process by which phosphopeptides bind to the 14-3-3ζ protein. Applying a novel scheme combining Hamiltonian replica exchange molecular dynamics and distancefield restraints allowed us to map and compare the most likely phosphopeptide-binding pathways to the 14-3-3ζ protein. The most important structural changes to the protein and peptides involved in the binding process were identified. In order to bind phosphopeptides to the primary interaction site, the 14-3-3ζ adopted a newly found wide-opened conformation. Based on our findings we additionally propose a secondary interaction site on the inner surface of the 14-3-3ζ dimer, and a direct interference on the binding process by the flexible C-terminal tail. A minimalistic model was designed to allow for the efficient calculation of absolute binding affinities. Binding affinities calculated from the potential of mean force along the binding pathway are in line with the available experimental estimates for two of the studied systems.
Collapse
Affiliation(s)
- Gabor Nagy
- CEITEC-MU, Masaryk University, Brno, Czech Republic
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jozef Hritz
- CEITEC-MU, Masaryk University, Brno, Czech Republic
- * E-mail:
| |
Collapse
|
9
|
Wieczorek M, Sticht J, Stolzenberg S, Günther S, Wehmeyer C, El Habre Z, Álvaro-Benito M, Noé F, Freund C. MHC class II complexes sample intermediate states along the peptide exchange pathway. Nat Commun 2016; 7:13224. [PMID: 27827392 PMCID: PMC5105163 DOI: 10.1038/ncomms13224] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 09/13/2016] [Indexed: 01/07/2023] Open
Abstract
The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Markov modelling analysis of an aggregate of 275 microseconds molecular dynamics simulations, we reveal that a stable pMHCII spontaneously samples intermediate conformations relevant for peptide exchange. More specifically, we observe two major peptide exchange pathways: the kinetic stability of a pMHCII's ground state defines its propensity for intrinsic peptide exchange, while the population of a rare, intermediate conformation correlates with the propensity of the HLA-DM-catalysed pathway. Helix-destabilizing mutants designed based on our model shift the exchange behaviour towards the HLA-DM-catalysed pathway and further allow us to conceptualize how allelic variation can shape an individual's MHC restricted immune response. MHCII proteins bind and present both foreign and self-antigens to potentially activate CD4+ T cells via cognate T cell receptors (TCRs) during the adaptive immune response. Here, the authors combine NMR-detected H/D exchange with Markov modelling analysis to shed light on the dynamics of MHCII peptide exchange.
Collapse
Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Sebastian Stolzenberg
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Sebastian Günther
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.,Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, Maryland 21201, USA
| | - Christoph Wehmeyer
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Zeina El Habre
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Frank Noé
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| |
Collapse
|
10
|
Graf MMH, Maurer M, Oostenbrink C. Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J Comput Chem 2016; 37:2597-605. [PMID: 27634475 PMCID: PMC5082540 DOI: 10.1002/jcc.24488] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 01/19/2023]
Abstract
Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2 /ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one-step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Michael M H Graf
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria
| | - Manuela Maurer
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190, Vienna, Austria.
| |
Collapse
|
11
|
Reif MM, Zacharias M. Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J Comput Chem 2016; 37:1711-24. [DOI: 10.1002/jcc.24390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Maria M. Reif
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
| | - Martin Zacharias
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
| |
Collapse
|
12
|
Graf MMH, Sucharitakul J, Bren U, Chu DB, Koellensperger G, Hann S, Furtmüller PG, Obinger C, Peterbauer CK, Oostenbrink C, Chaiyen P, Haltrich D. Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates. FEBS J 2015; 282:4218-41. [PMID: 26284701 PMCID: PMC4950071 DOI: 10.1111/febs.13417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 01/25/2023]
Abstract
Monomeric Agaricus meleagris pyranose dehydrogenase (AmPDH) belongs to the glucose-methanol-choline family of oxidoreductases. An FAD cofactor is covalently tethered to His103 of the enzyme. AmPDH can double oxidize various mono- and oligosaccharides at different positions (C1 to C4). To study the structure/function relationship of selected active-site residues of AmPDH pertaining to substrate (carbohydrate) turnover in more detail, several active-site variants were generated, heterologously expressed in Pichia pastoris, and characterized by biochemical, biophysical and computational means. The crystal structure of AmPDH shows two active-site histidines, both of which could take on the role as the catalytic base in the reductive half-reaction. Steady-state kinetics revealed that His512 is the only catalytic base because H512A showed a reduction in (kcat /KM )glucose by a factor of 10(5) , whereas this catalytic efficiency was reduced by two or three orders of magnitude for His556 variants (H556A, H556N). This was further corroborated by transient-state kinetics, where a comparable decrease in the reductive rate constant was observed for H556A, whereas the rate constant for the oxidative half-reaction (using benzoquinone as substrate) was increased for H556A compared to recombinant wild-type AmPDH. Steady-state kinetics furthermore indicated that Gln392, Tyr510, Val511 and His556 are important for the catalytic efficiency of PDH. Molecular dynamics (MD) simulations and free energy calculations were used to predict d-glucose oxidation sites, which were validated by GC-MS measurements. These simulations also suggest that van der Waals interactions are the main driving force for substrate recognition and binding.
Collapse
Affiliation(s)
- Michael M H Graf
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Urban Bren
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
- Laboratory for Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor, Slovenia
| | - Dinh Binh Chu
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
- School of Chemical Engineering, Department of Analytical Chemistry, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Austria
| | - Stephan Hann
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Paul G Furtmüller
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Christian Obinger
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Clemens K Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna (BOKU), Austria
| |
Collapse
|
13
|
Gasselhuber B, Carpena X, Graf MMH, Pirker KF, Nicolussi A, Sündermann A, Hofbauer S, Zamocky M, Furtmüller PG, Jakopitsch C, Oostenbrink C, Fita I, Obinger C. Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation. Biochemistry 2015; 54:5425-38. [DOI: 10.1021/acs.biochem.5b00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bernhard Gasselhuber
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Xavi Carpena
- Institut de Biologia Molecular (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michael M. H. Graf
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Katharina F. Pirker
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Nicolussi
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Axel Sündermann
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Stefan Hofbauer
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Biocenter 5, A-1030 Vienna, Austria
| | - Marcel Zamocky
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Institute
of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta
21, SK-84551 Bratislava, Slovakia
| | - Paul G. Furtmüller
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Christa Jakopitsch
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department
of Material Sciences and Process Engineering, Institute for Molecular
Modeling and Simulation, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Ignacio Fita
- Institut de Biologia Molecular (IBMB-CSIC), Parc Cientific de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Christian Obinger
- Department
of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| |
Collapse
|
14
|
Sittel F, Jain A, Stock G. Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates. J Chem Phys 2015; 141:014111. [PMID: 25005281 DOI: 10.1063/1.4885338] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Principal component analysis of molecular dynamics simulations is a popular method to account for the essential dynamics of the system on a low-dimensional free energy landscape. Using Cartesian coordinates, first the translation and overall rotation need to be removed from the trajectory. Since the rotation depends via the moment of inertia on the molecule's structure, this separation is only straightforward for relatively rigid systems. Adopting millisecond molecular dynamics simulations of the folding of villin headpiece and the functional dynamics of BPTI provided by D. E. Shaw Research, it is demonstrated via a comparison of local and global rotational fitting that the structural dynamics of flexible molecules necessarily results in a mixing of overall and internal motion. Even for the small-amplitude functional motion of BPTI, the conformational distribution obtained from a Cartesian principal component analysis therefore reflects to some extend the dominant overall motion rather than the much smaller internal motion of the protein. Internal coordinates such as backbone dihedral angles, on the other hand, are found to yield correct and well-resolved energy landscapes for both examples. The virtues and shortcomings of the choice of various fitting schemes and coordinate sets as well as the generality of these results are discussed in some detail.
Collapse
Affiliation(s)
- Florian Sittel
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University, 79104 Freiburg, Germany
| | - Abhinav Jain
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics and Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University, 79104 Freiburg, Germany
| |
Collapse
|
15
|
Graf MM, Zhixiong L, Bren U, Haltrich D, van Gunsteren WF, Oostenbrink C. Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation. PLoS Comput Biol 2014; 10:e1003995. [PMID: 25500811 DOI: 10.1371/journal.pcbi.1003995] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/13/2014] [Indexed: 11/19/2022] Open
Abstract
The flavoenzyme pyranose dehydrogenase (PDH) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications. A generalized approach to simulate all 32 possible aldohexopyranoses in the course of one or a few molecular dynamics (MD) simulations is reported. Free energy calculations according to the one-step perturbation (OSP) method revealed the solvation free energies (ΔGsolv) of all 32 aldohexopyranoses in water, which have not yet been reported in the literature. The free energy difference between β- and α-anomers (ΔGβ-α) of all d-stereoisomers in water were compared to experimental values with a good agreement. Moreover, the free-energy differences (ΔG) of the 32 stereoisomers bound to PDH in two different poses were calculated from MD simulations. The relative binding free energies (ΔΔGbind) were calculated and, where available, compared to experimental values, approximated from Km values. The agreement was very good for one of the poses, in which the sugars are positioned in the active site for oxidation at C1 or C2. Distance analysis between hydrogens of the monosaccharide and the reactive N5-atom of the flavin adenine dinucleotide (FAD) revealed that oxidation is possible at HC1 or HC2 for pose A, and at HC3 or HC4 for pose B. Experimentally detected oxidation products could be rationalized for the majority of monosaccharides by combining ΔΔGbind and a reweighted distance analysis. Furthermore, several oxidation products were predicted for sugars that have not yet been tested experimentally, directing further analyses. This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry. The results suggest that a similar approach could be applied to study promiscuity of other enzymes. Generally, enzymes are perceived as being specific for both their substrates and the reaction they catalyze. This standard paradigm started to shift and currently enzyme promiscuity towards various substrates is perceived rather as the rule than the exception. Enzyme promiscuity seems to be vital for proteins to acquire new functions, and therefore for evolution itself. The driving forces for promiscuity are manifold and consequently challenging to study. Binding free energies, which can be calculated from computer simulations, represent a convenient measure for them. Here, we investigate the binding free energies between the enzyme pyranose dehydrogenase (PDH) and a sugar-substrate by computational means. PDH has an extraordinarily promiscuous substrate-specificity, making it interesting for e.g. bioelectrochemical applications. By introducing modifications to the sugar-structure used for the molecular dynamics simulations, we could simultaneously study all 32 possible aldohexopyranoses from a single simulation. This saves costly computational resources and time for setting up and analyzing the simulations. We could nicely reproduce experimental results and predict so far undetected sugar-oxidation products, directing further experiments. This study gives novel insights into PDH's substrate promiscuity and the enzyme's applicability. A similar approach could be applied to study the promiscuity of other enzymes.
Collapse
|
16
|
Abstract
Aflatoxin B1 (AFB1)-the most potent natural carcinogen known to men-is metabolized by cytochrome P450 3A4 (CYP3A4), either to the genotoxic AFB1 exo-8,9-epoxide or to the detoxified 3α-hydroxy AFB1. The activation of the procarcinogen proceeds in a highly cooperative fashion, which differs from common allosteric regulation in the sense that it can be attributed to simultaneous occupancy of a single large and malleable active site by multiple ligand molecules. Unfortunately, unlike in the case of ketoconazole, there is currently no experimental structure available for the doubly ligated CYP3A4-AFB1 complex. Therefore, we employed a sequential molecular docking protocol to create various possible doubly ligated complexes and subsequently performed molecular dynamics simulations and free-energy calculations to check for their consistency with the available experimental data on regio- and stereoselectivity of both AFB1 oxidations as well as with available kinetic data. Only the system in which the first AFB1 molecule was bound in a face-on C8-C9 epoxidation mode and the second AFB1 molecule was bound in a side-on 3α-hydroxylation mode-a result of an unconstrained molecular docking protocol-has successfully fulfilled all the imposed criteria and is therefore proposed as the most likely structure of the doubly ligated complex of CYP3A4 with AFB1. The empirical Linear Interaction Energy method revealed that shape complementarity through nonpolar dispersion interactions between the two bound AFB1 molecules is the main source of the experimentally observed positive homotropic cooperativity. The reported study represents a nice example of how state-of-the-art molecular modeling techniques can be used to study complicated macromolecular complexes, whose structures have not yet been experimentally determined, and to validate these against the available experimental data. The proposed structure will facilitate future studies on the rational design of successful AFB1 modulators or on human subpopulations characterized by specific CYP3A4 polymorphisms that are especially sensitive to AFB1.
Collapse
Affiliation(s)
- Urban Bren
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, AT-1190 Vienna, Austria
| | | | | |
Collapse
|
17
|
Sündermann A, Reif MM, Hofbauer S, Obinger C, Oostenbrink C. Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations. Biochemistry 2014; 53:4869-79. [PMID: 24988286 PMCID: PMC4116397 DOI: 10.1021/bi500467h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Chlorite
dismutases are prokaryotic heme b oxidoreductases
that convert chlorite to chloride and dioxygen. It has been postulated
that during turnover hypochlorite is formed transiently, which might
be responsible for the observed irreversible inactivation of these
iron proteins. The only charged distal residue in the heme cavity
is a conserved and mobile arginine, but its role in catalysis and
inactivation is not fully understood. In the present study, the pentameric
chlorite dismutase (Cld) from the bacterium Candidatus Nitrospira
defluvii was probed for binding of the low spin ligand cyanide,
the substrate chlorite, and the intermediate hypochlorite. Simulations
were performed with the enzyme in the ferrous, ferric, and compound
I state. Additionally, the variant R173A was studied. We report the
parametrization for the GROMOS force field of the anions ClO–, ClO2–, ClO3–, and ClO4– and describe spontaneous
binding, unbinding, and rebinding events of chlorite and hypochlorite,
as well as the dynamics of the conformations of Arg173 during simulations.
The findings suggest that (i) chlorite binding to ferric NdCld occurs
spontaneously and (ii) that Arg173 is important for recognition and
to impair hypochlorite leakage from the reaction sphere. The simulation
data is discussed in comparison with experimental data on catalysis
and inhibition of chlorite dismutase.
Collapse
Affiliation(s)
- Axel Sündermann
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna , Muthgasse 18, A-1190 Vienna, Austria
| | | | | | | | | |
Collapse
|
18
|
Graf MM, Bren U, Haltrich D, Oostenbrink C. Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. J Comput Aided Mol Des 2013; 27:295-304. [PMID: 23591812 DOI: 10.1007/s10822-013-9645-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/04/2013] [Indexed: 11/11/2022]
Abstract
The flavin-dependent sugar oxidoreductase pyranose dehydrogenase (PDH) from the plant litter-degrading fungus Agaricus meleagris oxidizes d-glucose (GLC) efficiently at positions C2 and C3. The closely related pyranose 2-oxidase (P2O) from Trametes multicolor oxidizes GLC only at position C2. Consequently, the electron output per molecule GLC is twofold for PDH compared to P2O making it a promising catalyst for bioelectrochemistry or for introducing novel carbonyl functionalities into sugars. The aim of this study was to rationalize the mechanism of GLC dioxidation employing molecular dynamics simulations of GLC–PDH interactions. Shape complementarity through nonpolar van der Waals interactions was identified as the main driving force for GLC binding. Together with a very diverse hydrogen-bonding pattern, this has the potential to explain the experimentally observed promiscuity of PDH towards different sugars. Based on geometrical analysis, we propose a similar reaction mechanism as in P2O involving a general base proton abstraction, stabilization of the transition state, an alkoxide intermediate, through interaction with a protonated catalytic histidine followed by a hydride transfer to the flavin N5 atom. Our data suggest that the presence of the two potential catalytic bases His-512 and His-556 increases the versatility of the enzyme, by employing the most suitably oriented base depending on the substrate and its orientation in the active site. Our findings corroborate and rationalize the experimentally observed dioxidation of GLC by PDH and its promiscuity towards different sugars.
Collapse
|
19
|
Abstract
Cathepsins are mammalian papain-like cysteine proteases that play an important role in numerous physiological and pathological processes. In the present study, various molecular dynamics (MD) simulations of pro- and mature human cathepsins L and O were performed. This study is the first to report MD simulations to complement the initial model structure of (pro-)cathepsin O through conformational sampling, thus offering insight into the maturation of procathepsin O, which to date has not been described experimentally. The overall fold of (pro-)cathepsin O appears very similar to that of (pro-)cathepsin L. The propeptide binding loop (PBL)-propeptide interface of both procathepsins is found to form a stable two-stranded β-sheet. Additional stabilization of the PBL-propeptide interface is provided by hydrophobic side chain contacts in procathepsin L, whereas this seems to be due to charge-dipole interactions in procathepsin O. Introduction of two mutations (L147P and G148P) into procathepsin O entails a significant loss of hydrogen bonding, disabling formation of the interfacial β-sheet. Simulations at different protonation states suggest that procathepsin L is more sensitive to a change in pH than procathepsin O. Potential differences between the maturation of procathepsin O and procathepsin L inferred from the MD simulations might be caused by (i) stronger PBL-propeptide interactions in procathepsin O due to salt-bridge formation across the interface, (ii) more limited entropic gain of the propeptide of procathepsin O upon release into the bulk solvent due to diverse conformational states sampled in the bound state, (iii) more pronounced entropic loss of the PBL in procathepsin O upon substrate binding caused by diverse conformational states sampled in the free, mature enzyme, and (iv) lower sensitivity of procathepsin O to pH change caused by the presence of fewer carboxylate groups at the PBL-propeptide interface.
Collapse
Affiliation(s)
- Maria M Reif
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | | |
Collapse
|
20
|
Wassenaar TA, de Vries S, Bonvin AMJJ, Bekker H. SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. J Chem Theory Comput 2012; 8:3618-27. [PMID: 26593007 DOI: 10.1021/ct3000662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent-solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php .
Collapse
Affiliation(s)
- Tsjerk A Wassenaar
- Molecular Dynamics Group, Groningen Institute for Biotechnology and Biomolecular Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sjoerd de Vries
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Henk Bekker
- Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, POB 800, 9700 AV, Groningen, The Netherlands
| |
Collapse
|
21
|
Bren U, Oostenbrink C. Cytochrome P450 3A4 inhibition by ketoconazole: tackling the problem of ligand cooperativity using molecular dynamics simulations and free-energy calculations. J Chem Inf Model 2012; 52:1573-82. [PMID: 22587011 DOI: 10.1021/ci300118x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) metabolizes more than 50% of clinically used drugs and is often involved in adverse drug-drug interactions. It displays atypical binding and kinetic behavior toward a number of ligands characterized by a sigmoidal shape of the corresponding titration curves, which is indicative of a positive homotropic cooperativity. This requires a participation of at least two ligand molecules, whereby the binding of the first ligand molecule increases the affinity of CYP3A4 for the binding of the second ligand molecule. In the current study, a combination of molecular dynamics simulations and free-energy calculations was applied to elucidate the physicochemical origin of the observed positive homotropic cooperativity in ketoconazole binding to CYP3A4. The binding of the first ketoconazole molecule was established to increase the affinity for the binding of the second ketoconazole molecule by 5 kJ mol(-1), which explains and quantifies the experimentally observed cooperative behavior of CYP3A4. Shape complementarity through nonpolar van der Waals interactions was identified as the main driving force of this binding, which seems to be in line with the promiscuous nature of CYP3A4. Moreover, the calculated binding free energies were found to be in good agreement with the values predicted from a simple 2-ligand binding kinetic model as well as to successfully reproduce the experimental titration curve. This confirms the general applicability of rapid free-energy methods to study challenging biomolecular systems like cytochromes P450, which are characterized by a large flexibility and malleability of their active sites.
Collapse
Affiliation(s)
- Urban Bren
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, AT-1190 Vienna, Austria
| | | |
Collapse
|
22
|
Affiliation(s)
- Marc van Dijk
- Bijvoet Center for
Biomolecular
Research, Faculty of Science—Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Tsjerk A. Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute, Rijksuniversiteit
Groningen, Nijenborgh 7, 9747AG, The Netherlands
| | - Alexandre M.J.J. Bonvin
- Bijvoet Center for
Biomolecular
Research, Faculty of Science—Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
23
|
Aschi M, Amadei A, Pellegrino A, Perin N, Po’ R. Thermal and environmental effects on Oligothiophene low-energy singlet electronic excitations in dilute solution: a theoretical and experimental study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1177-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
24
|
Affiliation(s)
| | | | - Carsten Kutzner
- Computational Biomolecular Dynamics
Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Bert L. de Groot
- Computational Biomolecular Dynamics
Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
25
|
Anselmi M, Marocchi S, Aschi M, Amadei A. Theoretical modeling of the spectroscopic absorption properties of luciferin and oxyluciferin: A critical comparison with recent experimental studies. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
26
|
Anselmi M, Di Nola A, Amadei A. Kinetics of carbon monoxide migration and binding in solvated neuroglobin as revealed by molecular dynamics simulations and quantum mechanical calculations. J Phys Chem B 2011; 115:2436-46. [PMID: 21332165 DOI: 10.1021/jp110833v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neuroglobin (Ngb) is a globular protein that reversibly binds small ligands at the six coordination position of the heme. With respect to other globins similar to myoglobin, Ngb displays some peculiarities as the topological reorganization of the internal cavities coupled to the sliding of the heme, or the binding of the endogenous distal histidine to the heme in the absence of an exogenous ligand. In this Article, by using multiple (independent) molecular dynamics trajectories (about 500 ns in total), the migration pathways of photolized carbon monoxide (CO) within solvated Ngb were analyzed, and a quantitative description of CO migration and corresponding kinetics was obtained. MD results, combined with quantum mechanical calculations on the CO-heme binding-unbinding reaction step in Ngb, allowed construction of a quantitative model representing the relevant steps of CO migration and rebinding.
Collapse
|
27
|
|
28
|
Pochetti G, Mitro N, Lavecchia A, Gilardi F, Besker N, Scotti E, Aschi M, Re N, Fracchiolla G, Laghezza A, Tortorella P, Montanari R, Novellino E, Mazza F, Crestani M, Loiodice F. Structural insight into peroxisome proliferator-activated receptor gamma binding of two ureidofibrate-like enantiomers by molecular dynamics, cofactor interaction analysis, and site-directed mutagenesis. J Med Chem 2010; 53:4354-66. [PMID: 20462215 DOI: 10.1021/jm9013899] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular dynamics simulations were performed on two ureidofibrate-like enantiomers to gain insight into their different potency and efficacy against PPARgamma. The partial agonism of the S enantiomer seems to be due to its capability to stabilize different regions of the receptor allowing the interaction with both coactivators and corepressors as shown by fluorescence resonance energy transfer (FRET) assays. The recruitment of the corepressor N-CoR1 by the S enantiomer on two different responsive elements of PPARgamma regulated promoters was confirmed by chromatin immunoprecipitation assays. Cell-based transcription assays show that PPARgamma coactivator 1alpha (PGC-1alpha) and cAMP response element binding protein-binding protein (CBP) enhance the basal and ligand-stimulated receptor activity acting as coactivators of PPARgamma, whereas the receptor interacting protein 140 (RIP140) and the nuclear corepressor 1 (N-CoR1) repress the transcriptional activity of PPARgamma. We also tested the importance of the residue Q286 on the transcriptional activity of the receptor by site-directed mutagenesis and confirmed its key role in the stabilization of helix 12. Molecular modeling studies were performed to provide a molecular explanation for the different behavior of the mutants.
Collapse
Affiliation(s)
- Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Montelibretti, 00015 Monterotondo Stazione, Roma, Italia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Aschi M, Bozzi A, Di Bartolomeo R, Petruzzelli R. The role of disulfide bonds and N-terminus in the structural properties of hepcidins: Insights from molecular dynamics simulations. Biopolymers 2010; 93:917-26. [DOI: 10.1002/bip.21499] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
30
|
Zazza C, Palma A, Sanna N, Tatoli S, Aschi M. Computational Study on Compound I Redox-Active Species in Horseradish Peroxydase Enzyme: Conformational Fluctuations and Solvation Effects. J Phys Chem B 2010; 114:6817-24. [PMID: 20438084 DOI: 10.1021/jp101033w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Costantino Zazza
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Amedeo Palma
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Nico Sanna
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Simone Tatoli
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| | - Massimiliano Aschi
- CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Via dei Tizii, 6/b, 00185 Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, via Salaria Km. 29.3, Sez. Montelibretti, Monterotondo S.(RM), Italy, Dipartimento di Chimica, Università di Roma La Sapienza, P. le A. Moro 00185, Rome, Italy, and Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universita di L’Aquila, via Vetoio 67100, L’Aquila, Italy
| |
Collapse
|
31
|
Aschi M, Fontana A, Meo EMD, Zazza C, Amadei A. Characterization of Electronic Properties in Complex Molecular Systems: Modeling of a Micropolarity Probe. J Phys Chem B 2010; 114:1915-24. [DOI: 10.1021/jp909465f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy; Dipartimento di Scienze del Farmaco, Università “G. d’Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy; Supercomputing Center for University and Research, CASPUR, via dei Tizii 6/b, 00185 Rome, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Tor Vergata, via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Antonella Fontana
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy; Dipartimento di Scienze del Farmaco, Università “G. d’Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy; Supercomputing Center for University and Research, CASPUR, via dei Tizii 6/b, 00185 Rome, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Tor Vergata, via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Erika Maria Di Meo
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy; Dipartimento di Scienze del Farmaco, Università “G. d’Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy; Supercomputing Center for University and Research, CASPUR, via dei Tizii 6/b, 00185 Rome, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Tor Vergata, via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Costantino Zazza
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy; Dipartimento di Scienze del Farmaco, Università “G. d’Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy; Supercomputing Center for University and Research, CASPUR, via dei Tizii 6/b, 00185 Rome, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Tor Vergata, via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Andrea Amadei
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy; Dipartimento di Scienze del Farmaco, Università “G. d’Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy; Supercomputing Center for University and Research, CASPUR, via dei Tizii 6/b, 00185 Rome, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Tor Vergata, via della Ricerca Scientifica 1, I-00133 Rome, Italy
| |
Collapse
|
32
|
Zazza C, Palma A, Amadei A, Sanna N, Tatoli S, Aschi M. On the catalytic role of structural fluctuations in enzyme reactions: computational evidence on the formation of compound 0 in horseradish peroxidase. Faraday Discuss 2010. [DOI: 10.1039/b906614d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Aschi M, Fraschetti C, Filippi A, Speranza M. Reaction diastereoselectivity of chiral aminoalcohols/[Co(II)NO3]+ complexes in evaporating ESI nanodroplets: new insights from a joint experimental and computational investigation. J Mass Spectrom 2009; 44:1038-1046. [PMID: 19334002 DOI: 10.1002/jms.1577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The nature of the ionic species, formed by electrospray ionization (ESI) of Co(NO3)2/CH3OH solutions with a pair of aminoalcohols W and Y, has been investigated by mass spectrometric and computational methods. Collision induced dissociation (CID) of ions, formally corresponding to the [WYCoNO3]+ structures, yields fragmentation patterns which reflect not only the expected [WYCoNO3]+ connectivity but also that of other isomeric structures. Formation of these latter species is observed only in the presence of a tertiary aminoalcohol, like N-methylpseudoephedrine. The CID patterns are found to be strongly dependent on the chemical form (whether the free aminoalcohol or its hydrochloride), the configuration, and the relative concentration of the W and Y aminoalcohols. This variability parallels the results of classical MD (molecular dynamics) simulations of the [WYCoNO3]+ adducts which show a drastic alteration of the mechanical-dynamical features of the adducts by simply changing the charge state of W and/or Y, their absolute configuration, or by removing the solvent. The present experimental and computational study confirms the observation of fast stereoselective reactions in ESI nanodroplets before their evaporation and warns against any automatic correlation between the ESI spectrum of an analyte and its structure in solution.
Collapse
Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università dell'Aquila, 67010 Coppito, AQ, Italy
| | | | | | | |
Collapse
|
34
|
Winger M, Christen M, van Gunsteren WF. On the Conformational Properties of Amylose and Cellulose Oligomers in Solution. ACTA ACUST UNITED AC 2009; 2009:1-8. [DOI: 10.1155/2009/307695] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Molecular dynamics (MD) simulations were used to monitor the stability and
conformation of double-stranded and single-stranded amyloses and single-stranded
cellulose oligomers containing 9 sugar moieties in solution as a function of solvent
composition, ionic strength, temperature, and methylation state. This study along
with other previous studies suggests that hydrogen bonds are crucial for guaranteeing
the stability of the amylose double helix. Single-stranded amylose forms a helical
structure as well, and cellulose stays highly elongated throughout the simulation time, a
behavior that was also observed experimentally. In terms of coordination of solute
hydroxyl groups with ions, amylose shows entropy-driven coordination of calcium
and sulfate ions, whereas cellulose-ion coordination seems to be enthalpy-dominated.
This indicates that entropy considerations cannot be neglected when explaining the
structural differences between amyloses and celluloses.
Collapse
|
35
|
Tatoli S, Zazza C, Sanna N, Palma A, Aschi M. The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation. Biophys Chem 2009; 141:87-93. [DOI: 10.1016/j.bpc.2008.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/29/2008] [Accepted: 12/30/2008] [Indexed: 11/25/2022]
|
36
|
Amadei A, D’Alessandro M, D’Abramo M, Aschi M. Theoretical characterization of electronic states in interacting chemical systems. J Chem Phys 2009; 130:084109. [DOI: 10.1063/1.3080887] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
|
37
|
Zazza C, Mancini G, Sanna N, Aschi M. Thermodynamic features and environmental effects in a two-states molecular device under strict electrochemical control. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0523-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
38
|
Montanari R, Saccoccia F, Scotti E, Crestani M, Godio C, Gilardi F, Loiodice F, Fracchiolla G, Laghezza A, Tortorella P, Lavecchia A, Novellino E, Mazza F, Aschi M, Pochetti G. Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could be exploited for drug design. J Med Chem 2009; 51:7768-76. [PMID: 19053776 DOI: 10.1021/jm800733h] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors regulating glucose and lipid metabolism. The search for new PPAR ligands with reduced adverse effects with respect to the marketed antidiabetic agents thiazolidinediones (TZDs) and the dual-agonists glitazars is highly desired. We report the crystal structure and activity of the two enantiomeric forms of a clofibric acid analogue, respectively complexed with the ligand-binding domain (LBD) of PPARgamma, and provide an explanation on a molecular basis for their different potency and efficacy against PPARgamma. The more potent S-enantiomer is a dual PPARalpha/PPARgamma agonist which presents a partial agonism profile against PPARgamma. Docking of the S-enantiomer in the PPARalpha-LBD has been performed to explain its different subtype pharmacological profile. The hypothesis that partial agonists show differential stabilization of helix 3, when compared to full agonists, is also discussed. Moreover, the structure of the complex with the S-enantiomer reveals a new region of the PPARgamma-LBD never sampled before by other ligands.
Collapse
|
39
|
Amadei A, Aschi M, Nola AD. Statistical Mechanical Modeling of Chemical Reactions in Condensed Phase Systems. In: Canuto S, editor. Solvation Effects on Molecules and Biomolecules. Dordrecht: Springer Netherlands; 2008. pp. 191-213. [DOI: 10.1007/978-1-4020-8270-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
|
40
|
Bozzi A, Mangoni ML, Rinaldi AC, Mignogna G, Aschi M. Folding propensity and biological activity of peptides: the effect of a single stereochemical isomerization on the conformational properties of bombinins in aqueous solution. Biopolymers 2008; 89:769-78. [PMID: 18459169 DOI: 10.1002/bip.21006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Folding propensities of bombinins H2 and H4, two members of amphibian bombinins H, a family of 17-20 residue alpha-helical peptides, have been investigated by means of circular dichroism (CD) measurements and molecular dynamics (MD) simulations. The two peptides, with primary structure IIGPVLGLVGSALGGLLKKI-NH2 and differing only for the configuration of the second aminoacid (an L-isoleucine in H2 and a D-alloisoleucine in H4) behave rather differently in solution. In particular both CD measurements and MD simulations indicate that bombinin H2 shows a markedly higher tendency to fold. From a careful inspection of MD trajectories it emerges that the stereochemical isomerization mutation of residue 2 to D-alloisoleucine in H4 peptide, drastically decreases its ability to form intrapeptide contacts. MD simulations also indicate that the conformational sampling in both systems derives from a subtle combination of energetic and entropic effects both involving the peptide itself and the solvent. The present results have been finally paralleled with preliminary information on bombinins H2 and H4 biological activity, i.e. interaction with membrane, supporting the hypothesis of an "already folded" conformation in water rather than interfacial folding tenet.
Collapse
Affiliation(s)
- Argante Bozzi
- Dipartimento di Scienze e Tecnologie Biomediche, Università L'Aquila e Consorzlo INBB, Italy
| | | | | | | | | |
Collapse
|
41
|
Zazza C, Amadei A, Palma A, Sanna N, Tatoli S, Aschi M. Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase. J Phys Chem B 2008; 112:3184-92. [DOI: 10.1021/jp0774692] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Costantino Zazza
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Andrea Amadei
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Amedeo Palma
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Nico Sanna
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Simone Tatoli
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| | - Massimiliano Aschi
- Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca (CASPUR), Via dei Tizii 6b, 00185 Roma, Italy, Dipartimento di Chimica, Ingegneria Chimica e Materiali Università di L'Aquila, via Vetoio 67100, L'Aquila, Italy, Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica 1 I-00133, Roma, Italy, Istituto per lo Studio dei Materiali Nanostrutturati, CNR-ISMN, Via Salaria km 29.3, Sez. Montelibretti, Monterotondo S. (RM
| |
Collapse
|
42
|
Wassenaar TA, Quax WJ, Mark AE. The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study. Proteins 2008; 70:333-43. [PMID: 17671978 DOI: 10.1002/prot.21541] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Death Receptor 5 (DR5), a member of tumor necrosis factor receptor (TNFR) superfamily of receptors, triggers apoptosis (programmed cell death) when stimulated by its tridentate ligand TRAIL. Until recently it was generally assumed that the activation of DR5 resulted from the recruitment of three independent receptor units, leading to the trimerization of intracellular domains. However, there is mounting evidence to suggest that, in the absence of ligand, such cytokine receptors primarily reside as preformed complexes. In this work, molecular dynamics simulations of the TRAIL-DR5 complex, the unbound receptor trimer and individual receptor monomers are compared to gain insight in the mechanism of activation. The results suggest that, in the absence of TRAIL, DR5 has a strong propensity to self-associate and that this is primarily mediated through interactions of the membrane proximal domains. The association of the free receptors leads to a loss of the threefold symmetry found within the receptor-ligand complex. The simulations suggest that the primary role of TRAIL is to induce threefold-symmetry within the DR5 complex and to constrain the receptor to a specific conformation. The implications of this in terms of the mechanism by which the receptor switches from an inactive to an active state are discussed.
Collapse
Affiliation(s)
- Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, 9747AG Groningen, The Netherlands
| | | | | |
Collapse
|
43
|
Aschi M, D’Alessandro M, Pellegrino M, Nola AD, D’Abramo M, Amadei A. Intramolecular charge transfer in π-conjugated oligomers: a theoretical study on the effect of temperature and oxidation state. Theor Chem Acc 2008. [DOI: 10.1007/s00214-007-0407-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
44
|
Anselmi M, Brunori M, Vallone B, Di Nola A. Molecular dynamics simulation of deoxy and carboxy murine neuroglobin in water. Biophys J 2007; 93:434-41. [PMID: 17468165 PMCID: PMC1896225 DOI: 10.1529/biophysj.106.099648] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 03/26/2007] [Indexed: 11/18/2022] Open
Abstract
Globins are respiratory proteins that reversibly bind dioxygen and other small ligands at the iron of a heme prosthetic group. Hemoglobin and myoglobin are the most prominent members of this protein family. Unexpectedly a few years ago a new member was discovered and called neuroglobin (Ngb), being predominantly expressed in the brain. Ngb is a single polypeptide of 151 amino acids and despite the small sequence similarity with other globins, it displays the typical globin fold. Oxygen, nitric oxide, or carbon monoxide can displace the distal histidine which, in ferrous Ngb as well as in ferric Ngb, is bound to the iron, yielding a reversible adduct. Recent crystallographic data on carboxy Ngb show that binding of an exogenous ligand is associated to structural changes involving heme sliding and a topological reorganization of the internal cavities; in particular, the huge internal tunnel that connects the bulk with the active site, peculiar to Ngb, is heavily reorganized. We report the results of extended (90 ns) molecular dynamics simulations in water of ferrous deoxy and carboxy murine neuroglobin, which are both coordinated on the distal site, in the latter case by CO and in the former one by the distal His(64)(E7). The long timescale of the simulations allowed us to characterize the equilibrated protein dynamics and to compare protein structure and dynamical behavior coupled to the binding of an exogenous ligand. We have characterized the heme sliding motion, the topological reorganization of the internal cavities, the dynamics of the distal histidine, and particularly the conformational change of the CD loop, whose flexibility depends ligand binding.
Collapse
|
45
|
D’abramo M, Aschi M, Marinelli F, Di Nola A, Amadei A. Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water. ACTA ACUST UNITED AC 2007; 811:197-201. [DOI: 10.1016/j.theochem.2007.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Abstract
In this article we use the perturbed matrix method and an extended molecular dynamics sampling of the carbon monoxide (CO) in the myoglobin distal pocket to characterize the CO vibrational spectrum and hence to relate its spectroscopic features with the atomic-molecular behavior. Results show the accuracy of the method employed and confirm the assignment of the spectroscopic B1 and B2 states proposed by Lim et al.
Collapse
|
47
|
Amadei A, D’Abramo M, Nola AD, Arcadi A, Cerichelli G, Aschi M. Theoretical study of intramolecular charge transfer in π-conjugated oligomers. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
48
|
Amadei A, D’Abramo M, Daidone I, D’Alessandro M, Nola AD, Aschi M. Statistical mechanical modelling of chemical reactions in complex systems: the kinetics of the Haem carbon monoxide binding–unbinding reaction in Myoglobin. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0197-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
49
|
Bozzi A, Coccia C, Di Giulio A, Rinaldi AC, Amadei A, Mignogna G, Bonamore A, Fais A, Aschi M. Folding propensity and biological activity of peptides: New insights from conformational properties of a novel peptide derived fromVitreoscilla haemoglobin. Biopolymers 2007; 87:85-92. [PMID: 17554783 DOI: 10.1002/bip.20792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The synthetic peptide Vitr-p-13 (YPIVGQELLGAIK-NH(2)), derived from the bacterial dimeric Vitreoscilla haemoglobin (VHb) in the position 95-107, is characterized by a pre-eminent "statistical coil" conformation in water as demonstrated by CD experiments and long time-scale MD simulations. In particular, Vitr-p-13 does not spontaneously adopt an alpha-helix folding in water, but it is rather preferentially found in beta-hairpin-like conformations. Long time-scale MD simulations have also shown that Vitr-p-13 displays a "topological-trigger" which initiates alpha-helix folding within residues 7-10, exactly like seen in the temporins, a group of linear, membrane-active antimicrobial peptides of similar length. At variance with temporins, in Vitr-p-13 such a process is energetically very demanding (+10 kJ/mol) in water at 300 K, and the peptide was found to be unable to bind model membranes in vitro and was devoid of antimicrobial activity. The present results, compared with previous studies on similar systems, strengthen the hypothesis of the requirement of a partial folding when still in aqueous environment to allow a peptide to interact with cell-membranes and eventually exert membrane perturbation-related antibiotic effects on target microbial cells.
Collapse
Affiliation(s)
- A Bozzi
- Dipartimento di Scienze e Tecnologie Biomediche, Università de L'Aquila, Italia
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Aschi M, Besker N, Re N, Pochetti G, Coletti C, Gallina C, Mazza F. Stereoselectivity by Enantiomeric Inhibitors of Matrix Metalloproteinase-8: New Insights from Molecular Dynamics Simulations. J Med Chem 2006; 50:211-8. [PMID: 17228863 DOI: 10.1021/jm0608457] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular Dynamics simulations in aqueous solution were performed for the matrix metalloproteinase-8 (MMP-8) free catalytic domain and for its complexes with the (R)- and (S)-[1-(4'-methoxybiphenyl-4-sulfonylamino)-2-methylpropyl] phosphonate. The 144-155 loop of the enzyme undergoes a drastic decrease of mobility once complexed with both enantiomers. The two enantiomers induce a different decrease of conformational entropy upon complexation. The higher affinity of the R-enantiomer can be related to the lower loss of conformational entropy accompanying its binding. The differences in the dynamical behavior of the protein induced by the two enantiomers are discussed at molecular level and the mode of binding of the simulated complexes is compared with that previously determined by X-ray crystallography.
Collapse
Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università di L'Aquila, Italia.
| | | | | | | | | | | | | |
Collapse
|