1
|
Solov'yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov'yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024. [PMID: 38842266 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
Collapse
Affiliation(s)
- Andrey V Solov'yov
- MBN Research Center, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | | | - Nigel J Mason
- School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, United Kingdom
| | - Richard A Amos
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre for Light Matter Interactions, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Sciences Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European Innovation Center, Bořivojova 2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Kate Ricketts
- Department of Targeted Intervention, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E H Wheatley
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| |
Collapse
|
2
|
Laurien M, Mende L, Luhrmann L, Frederiksen A, Aldag M, Spiecker L, Clemmesen C, Solov'yov IA, Gerlach G. Magnetic orientation in juvenile Atlantic herring ( Clupea harengus) could involve cryptochrome 4 as a potential magnetoreceptor. J R Soc Interface 2024; 21:20240035. [PMID: 38835248 DOI: 10.1098/rsif.2024.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/06/2024] Open
Abstract
The Earth's magnetic field can provide reliable directional information, allowing migrating animals to orient themselves using a magnetic compass or estimate their position relative to a target using map-based orientation. Here we show for the first time that young, inexperienced herring (Clupea harengus, Ch) have a magnetic compass when they migrate hundreds of kilometres to their feeding grounds. In birds, such as the European robin (Erithacus rubecula), radical pair-based magnetoreception involving cryptochrome 4 (ErCRY4) was demonstrated; the molecular basis of magnetoreception in fish is still elusive. We show that cry4 expression in the eye of herring is upregulated during the migratory season, but not before, indicating a possible use for migration. The amino acid structure of herring ChCRY4 shows four tryptophans and a flavin adenine dinucleotide-binding site, a prerequisite for a magnetic receptor. Using homology modelling, we successfully reconstructed ChCRY4 of herring, DrCRY4 of zebrafish (Danio rerio) and StCRY4 of brown trout (Salmo trutta) and showed that ChCRY4, DrCRY4 and ErCRY4a, but not StCRY4, exhibit very comparable dynamic behaviour. The electron transfer could take place in ChCRY4 in a similar way to ErCRY4a. The combined behavioural, transcriptomic and simulation experiments provide evidence that CRY4 could act as a magnetoreceptor in Atlantic herring.
Collapse
Affiliation(s)
- Malien Laurien
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lara Mende
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lena Luhrmann
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Anders Frederiksen
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Mandus Aldag
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lisa Spiecker
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Catriona Clemmesen
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel 24105, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Gabriele Gerlach
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| |
Collapse
|
3
|
Finke F, Hungerland J, Solov'yov IA, Schuhmann F. Different receptor models show differences in ligand binding strength and location: a computational drug screening for the tick-borne encephalitis virus. Mol Divers 2024:10.1007/s11030-024-10850-8. [PMID: 38739227 DOI: 10.1007/s11030-024-10850-8] [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: 02/09/2024] [Accepted: 03/16/2024] [Indexed: 05/14/2024]
Abstract
The tick-borne encephalitis virus (TBE) is a neurotrophic disease that has spread more rapidly throughout Europe and Asia in the past few years. At the same time, no cure or specific therapy is known to battle the illness apart from vaccination. To find a pharmacologically relevant drug, a computer-aided drug screening was initiated. Such a procedure probes a possible binding of a drug to the RNA Polymerase of TBE. The crystal structure of the receptor, however, includes missing and partially modeled regions, which rendered the structure incomplete and of questionable use for a thorough drug screening procedure. The quality of the receptor model was addressed by studying three putative structures created. We show that the choice of receptor models greatly influences the binding affinity of potential drug molecules and that the binding location could also be significantly impacted. We demonstrate that some drug candidates are unsuitable for one model but show decent results for another. Without any prejudice on the three employed receptor models, the study reveals the imperative need to investigate the receptor structure before drug binding is probed whether experimentally or computationally.
Collapse
Affiliation(s)
- Felicitas Finke
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Jonathan Hungerland
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
- Research Centre for Neurosensory Science, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany.
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany.
| | - Fabian Schuhmann
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| |
Collapse
|
4
|
Langebrake C, Manthey G, Frederiksen A, Lugo Ramos JS, Dutheil JY, Chetverikova R, Solov'yov IA, Mouritsen H, Liedvogel M. Adaptive evolution and loss of a putative magnetoreceptor in passerines. Proc Biol Sci 2024; 291:20232308. [PMID: 38320616 PMCID: PMC10846946 DOI: 10.1098/rspb.2023.2308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magnetic sensitivity in vitro compared to Cry4a from resident species. We investigate Cry and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes and identifies different selection regimes in passerines. We show that Cry4a is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that are likely to have facilitated the evolution of an optimized sensory protein for night-time orientation in songbirds. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines), and thus identified a gene deletion, which might facilitate testing the function of Cry4a in birds. In contrast, the other avian Cry (Cry1 and Cry2) were highly conserved across all species, indicating basal, non-sensory functions. Our results support a specialization or functional differentiation of Cry4 in songbirds which could be magnetosensation.
Collapse
Affiliation(s)
- Corinna Langebrake
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Georg Manthey
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Juan S. Lugo Ramos
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- The Francis Crick Institute, London NW1 1AT, UK
| | - Julien Y. Dutheil
- Research Group Molecular Systems Evolution, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Raisa Chetverikova
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Ilia A. Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Henrik Mouritsen
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Miriam Liedvogel
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| |
Collapse
|
5
|
Stephani J, Gerhards L, Khairalla B, Solov’yov IA, Brand I. How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration. ACS Infect Dis 2024; 10:763-778. [PMID: 38259029 PMCID: PMC10862549 DOI: 10.1021/acsinfecdis.3c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.
Collapse
Affiliation(s)
- Justus
C. Stephani
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Bishoy Khairalla
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
- Research
Center Neurosensory Science, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
- CeNaD—Center
for Nanoscale Dynamics, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| |
Collapse
|
6
|
Jacobsen L, Hungerland J, Bačić V, Gerhards L, Schuhmann F, Solov’yov IA. Introducing the Automated Ligand Searcher. J Chem Inf Model 2023; 63:7518-7528. [PMID: 37983165 PMCID: PMC10716895 DOI: 10.1021/acs.jcim.3c01317] [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: 08/21/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/22/2023]
Abstract
The Automated Ligand Searcher (ALISE) is designed as an automated computational drug discovery tool. To approximate the binding free energy of ligands to a receptor, ALISE includes a three-stage workflow, with each stage involving an increasingly sophisticated computational method: molecular docking, molecular dynamics, and free energy perturbation, respectively. To narrow the number of potential ligands, poorly performing ligands are gradually segregated out. The performance and usability of ALISE are benchmarked for a case study containing known active ligands and decoys for the HIV protease. The example illustrates that ALISE filters the decoys successfully and demonstrates that the automation, comprehensiveness, and user-friendliness of the software make it a valuable tool for improved and faster drug development workflows.
Collapse
Affiliation(s)
- Luise Jacobsen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jonathan Hungerland
- Institute
of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Vladimir Bačić
- Institute
of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Fabian Schuhmann
- Institute
of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Niels
Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| |
Collapse
|
7
|
Code C, Qiu D, Solov’yov IA, Lee JG, Shin HC, Roland C, Sagui C, Houde D, Rand KD, Jørgensen TJD. Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties. J Am Chem Soc 2023; 145:23925-23938. [PMID: 37883679 PMCID: PMC10636759 DOI: 10.1021/jacs.3c04068] [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: 04/19/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.
Collapse
Affiliation(s)
- Christian Code
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Danwen Qiu
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department
of Physics, Carl von Ossietzky University
Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Jung-Goo Lee
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Hyeon-Cheol Shin
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Christopher Roland
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Damian Houde
- Department
of Protein Pharmaceutical Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| |
Collapse
|
8
|
Vu HH, Behrmann H, Hanić M, Jeyasankar G, Krishnan S, Dannecker D, Hammer C, Gunkel M, Solov'yov IA, Wolf E, Behrmann E. A marine cryptochrome with an inverse photo-oligomerization mechanism. Nat Commun 2023; 14:6918. [PMID: 37903809 PMCID: PMC10616196 DOI: 10.1038/s41467-023-42708-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark, PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishes PdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight.
Collapse
Affiliation(s)
- Hong Ha Vu
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Heide Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
| | - Gayathri Jeyasankar
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Shruthi Krishnan
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Dennis Dannecker
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Constantin Hammer
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Monika Gunkel
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111, Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
| | - Elmar Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany.
| |
Collapse
|
9
|
Khan M, Kandwal S, Fayne D. DataPype: A Fully Automated Unified Software Platform for Computer-Aided Drug Design. ACS OMEGA 2023; 8:39468-39480. [PMID: 37901539 PMCID: PMC10601415 DOI: 10.1021/acsomega.3c05207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023]
Abstract
With the advent of computer-aided drug design (CADD), traditional physical testing of thousands of molecules has now been replaced by target-focused drug discovery, where potentially bioactive molecules are predicted by computer software before their physical synthesis. However, despite being a significant breakthrough, CADD still faces various limitations and challenges. The increasing availability of data on small molecules has created a need to streamline the sourcing of data from different databases and automate the processing and cleaning of data into a form that can be used by multiple CADD software applications. Several standalone software packages are available to aid the drug designer, each with its own specific application, requiring specialized knowledge and expertise for optimal use. These applications require their own input and output files, making it a challenge for nonexpert users or multidisciplinary discovery teams. Here, we have developed a new software platform called DataPype, which wraps around these different software packages. It provides a unified automated workflow to search for hit compounds using specialist software. Additionally, multiple virtual screening packages can be used in the one workflow, and if different ways of looking at potential hit compounds all predict the same set of molecules, we have higher confidence that we should make or purchase and test the molecules. Importantly, DataPype can run on computer servers, speeding up the virtual screening for new compounds. Combining access to multiple CADD tools within one interface will enhance the early stage of drug discovery, increase usability, and enable the use of parallel computing.
Collapse
Affiliation(s)
- Mohemmed
Faraz Khan
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow U.P., 226026, India
| | - Shubhangi Kandwal
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Darren Fayne
- Molecular
Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|
10
|
Frederiksen A, Langebrake C, Hanić M, Manthey G, Mouritsen H, Liedvogel M, Solov’yov IA. Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a. ACS OMEGA 2023; 8:26425-26436. [PMID: 37521624 PMCID: PMC10373462 DOI: 10.1021/acsomega.3c02963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
The ability of migratory birds to sense magnetic fields has been known for decades, although the understanding of the underlying mechanism is still elusive. Currently, the strongest magnetoreceptor candidate in birds is a protein called cryptochrome 4a. The cryptochrome 4a protein has changed through evolution, apparently endowing some birds with a more pronounced magnetic sensitivity than others. Using phylogenetic tools, we show that a specific tryptophan tetrad and a tyrosine residue predicted to be essential for cryptochrome activation are highly conserved in the avian clade. Through state-of-the-art molecular dynamics simulations and associated analyses, we also studied the role of these specific residues and the associated mutants on the overall dynamics of the protein. The analyses of the single residue mutations were used to judge how far a local change in the protein structure can impact specific dynamics of European robin cryptochrome 4a. We conclude that the replacements of each of the tryptophans one by one with a phenylalanine do not compromise the overall stability of the protein.
Collapse
Affiliation(s)
- Anders Frederiksen
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Corinna Langebrake
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Maja Hanić
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Georg Manthey
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Henrik Mouritsen
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Miriam Liedvogel
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- MPRG
Behavioural Genomics, Max Planck Institute
for Evolutionary Biology, August-Thienemann-Str. 2, Plön 24306, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Department
of Physics, Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
| |
Collapse
|
11
|
Hanić M, Antill LM, Gehrckens AS, Schmidt J, Görtemaker K, Bartölke R, El-Baba TJ, Xu J, Koch KW, Mouritsen H, Benesch JLP, Hore PJ, Solov'yov IA. Dimerization of European Robin Cryptochrome 4a. J Phys Chem B 2023. [PMID: 37428840 PMCID: PMC10364083 DOI: 10.1021/acs.jpcb.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Homo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observed in vitro for European robin Cry4a, little is known about the dimerization of avian Crys and the role it could play in the mechanism of magnetic sensing in migratory birds. Here, we present a combined experimental and computational investigation of the dimerization of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulfide bonds, chemical cross-linking, and photometric measurements show that disulfide-linked dimers are routinely formed, that their formation is promoted by exposure to blue light, and that the most likely cysteines are C317 and C412. Computational modeling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.
Collapse
Affiliation(s)
- Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Lewis M Antill
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura Ward, Saitama 338-8570, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Angela S Gehrckens
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jessica Schmidt
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Katharina Görtemaker
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
| | - Rabea Bartölke
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Tarick J El-Baba
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - P J Hore
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
| |
Collapse
|
12
|
Grüning G, Wong SY, Gerhards L, Schuhmann F, Kattnig DR, Hore PJ, Solov’yov IA. Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes. J Am Chem Soc 2022; 144:22902-22914. [DOI: 10.1021/jacs.2c06233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Gesa Grüning
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Siu Ying Wong
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Fabian Schuhmann
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Daniel R. Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - P. J. Hore
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Ilia A. Solov’yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Institut für Physik, Ammerländer Heerstreet 114-118, 26129 Oldenburg, Germany
| |
Collapse
|
13
|
Solov'yov IA, Sushko G, Friis I, Solov'yov AV. Multiscale modeling of stochastic dynamics processes with MBN Explorer. J Comput Chem 2022; 43:1442-1458. [PMID: 35708151 DOI: 10.1002/jcc.26948] [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: 03/29/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/09/2022]
Abstract
Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN Explorer. Stochastic dynamics in MBN Explorer relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with MBN Explorer.
Collapse
Affiliation(s)
- Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Oldenburg, Germany.,Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.,Center for Nanoscale Dynamics (CENAD), Institut für Physik, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | | | - Ida Friis
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | | |
Collapse
|
14
|
Hanić M, Schuhmann F, Frederiksen A, Langebrake C, Manthey G, Liedvogel M, Xu J, Mouritsen H, Solov'yov IA. Computational Reconstruction and Analysis of Structural Models of Avian Cryptochrome 4. J Phys Chem B 2022; 126:4623-4635. [PMID: 35704801 DOI: 10.1021/acs.jpcb.2c00878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recent study by Xu et al. (Nature, 2021, 594, 535-540) provided strong evidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magnetic compass sense. The investigation compared the magnetic field response of Cry4 from migratory and nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist. This finding prompted an in-depth investigation into Cry4 protein differences on the structural and dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used to reconstruct the missing avian Cry4 protein structures via homology modeling for carefully selected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap, zebra finch, chicken, and pigeon were subsequently simulated dynamically and analyzed. The studied avian Cry4 structures show flexibility in analogous regions pointing to similar activation mechanisms and/or signaling interaction partners. It can be concluded that the experimentally recorded difference in the magnetic field sensitivity of Cry4 from different birds is unlikely to be due to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified.
Collapse
Affiliation(s)
- Maja Hanić
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Fabian Schuhmann
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Corinna Langebrake
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Georg Manthey
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Miriam Liedvogel
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany.,Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| |
Collapse
|
15
|
Shahu MK, Schuhmann F, Scholten A, Solov’yov IA, Koch KW. The Transition of Photoreceptor Guanylate Cyclase Type 1 to the Active State. Int J Mol Sci 2022; 23:ijms23074030. [PMID: 35409388 PMCID: PMC8999790 DOI: 10.3390/ijms23074030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/02/2022] [Indexed: 11/16/2022] Open
Abstract
Membrane-bound guanylate cyclases (GCs), which synthesize the second messenger guanosine-3', 5'-cyclic monophosphate, differ in their activation modes to reach the active state. Hormone peptides bind to the extracellular domain in hormone-receptor-type GCs and trigger a conformational change in the intracellular, cytoplasmic part of the enzyme. Sensory GCs that are present in rod and cone photoreceptor cells have intracellular binding sites for regulatory Ca2+-sensor proteins, named guanylate-cyclase-activating proteins. A rotation model of activation involving an α-helix rotation was described as a common activation motif among hormone-receptor GCs. We tested whether the photoreceptor GC-E underwent an α-helix rotation when reaching the active state. We experimentally simulated such a transitory switch by integrating alanine residues close to the transmembrane region, and compared the effects of alanine integration with the point mutation V902L in GC-E. The V902L mutation is found in patients suffering from retinal cone-rod dystrophies, and leads to a constitutively active state of GC-E. We analyzed the enzymatic catalytic parameters of wild-type and mutant GC-E. Our data showed no involvement of an α-helix rotation when reaching the active state, indicating a difference in hormone receptor GCs. To characterize the protein conformations that represent the transition to the active state, we investigated the protein dynamics by using a computational approach based on all-atom molecular dynamics simulations. We detected a swinging movement of the dimerization domain in the V902L mutant as the critical conformational switch in the cyclase going from the low to high activity state.
Collapse
Affiliation(s)
- Manisha Kumari Shahu
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, 26111 Oldenburg, Germany; (M.K.S.); (A.S.)
| | - Fabian Schuhmann
- Institute of Physics, University of Oldenburg, 26111 Oldenburg, Germany; (F.S.); (I.A.S.)
| | - Alexander Scholten
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, 26111 Oldenburg, Germany; (M.K.S.); (A.S.)
| | - Ilia A. Solov’yov
- Institute of Physics, University of Oldenburg, 26111 Oldenburg, Germany; (F.S.); (I.A.S.)
- Research Centre for Neurosensory Science, University of Oldenburg, 26111 Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Division of Biochemistry, Department of Neuroscience, University of Oldenburg, 26111 Oldenburg, Germany; (M.K.S.); (A.S.)
- Research Centre for Neurosensory Science, University of Oldenburg, 26111 Oldenburg, Germany
- Correspondence:
| |
Collapse
|
16
|
Schuhmann F, Kattnig DR, Solov'yov IA. Exploring Post-activation Conformational Changes in Pigeon Cryptochrome 4. J Phys Chem B 2021; 125:9652-9659. [PMID: 34327996 DOI: 10.1021/acs.jpcb.1c02795] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A widespread hypothesis ascribes the ability of migratory birds to navigate over large distances to an inclination compass realized by the protein cryptochrome in the birds' retinae. Cryptochromes are activated by blue light, which induces a radical pair state, the spin dynamics of which may become sensitive to earth's weak magnetic fields. The magnetic information is encoded and passed on to downstream processes by structural rearrangements of the protein, the details of which remain vague. We utilize extensive all-atom molecular dynamics simulations to probe the conformational changes of pigeon cryptochrome 4 upon light activation. The structural dynamics are analyzed based on principal component analysis and with the help of distance matrices, which reveal significant changes in selected inter-residue distances. The results are evaluated and discussed with reference to the protein structure and its putative function as a magnetoreceptor. It is suggested that the phosphate-binding loop could act as a gate controlling the access to the flavin adenine dinucleotide cofactor depending on the redox state of the protein.
Collapse
Affiliation(s)
- Fabian Schuhmann
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Rd., Exeter EX4 4QD, U.K
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
| |
Collapse
|
17
|
Husen P, Solov'yov IA. Modeling the Energy Landscape of Side Reactions in the Cytochrome bc 1 Complex. Front Chem 2021; 9:643796. [PMID: 34095083 PMCID: PMC8170094 DOI: 10.3389/fchem.2021.643796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Much of the metabolic molecular machinery responsible for energy transduction processes in living organisms revolves around a series of electron and proton transfer processes. The highly redox active enzymes can, however, also pose a risk of unwanted side reactions leading to reactive oxygen species, which are harmful to cells and are a factor in aging and age-related diseases. Using extensive quantum and classical computational modeling, we here show evidence of a particular superoxide production mechanism through stray reactions between molecular oxygen and a semiquinone reaction intermediate bound in the mitochondrial complex III of the electron transport chain, also known as the cytochrome b c 1 complex. Free energy calculations indicate a favorable electron transfer from semiquinone occurring at low rates under normal circumstances. Furthermore, simulations of the product state reveal that superoxide formed at the Q o -site exclusively leaves the b c 1 complex at the positive side of the membrane and escapes into the intermembrane space of mitochondria, providing a critical clue in further studies of the harmful effects of mitochondrial superoxide production.
Collapse
Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| |
Collapse
|
18
|
Schuhmann F, Korol V, Solov'yov IA. Introducing Pep McConst-A user-friendly peptide modeler for biophysical applications. J Comput Chem 2021; 42:572-580. [PMID: 33426653 DOI: 10.1002/jcc.26479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023]
Abstract
We are introducing Pep McConst-a software that employs a Monte-Carlo algorithm to construct 3D structures of polypeptide chains which could subsequently be studied as stand-alone macromolecules or complement the structure of known proteins. Using an approach to avoid steric clashes, Pep McConst allows to create multiple structures for a predefined primary sequence of amino acids. These structures could then effectively be used for further structural analysis and investigations. The article introduces the algorithm and describes its user-friendly approach that was made possible through the VIKING online platform. Finally, the manuscript provides several highlight examples where Pep McConst was used to predict the structure of the C-terminal of a known protein, generate a missing bit of already crystallized protein structures and simply generate short polypeptide chains.
Collapse
Affiliation(s)
- Fabian Schuhmann
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Oldenburg, Germany
| | - Vasili Korol
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universät Oldenburg, Oldenburg, Germany
| |
Collapse
|
19
|
Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
Collapse
Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
20
|
Sjulstok E, Solov'yov IA. Structural Explanations of Flavin Adenine Dinucleotide Binding in Drosophila melanogaster Cryptochrome. J Phys Chem Lett 2020; 11:3866-3870. [PMID: 32330039 DOI: 10.1021/acs.jpclett.0c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cryptochrome proteins are thought to be involved in light-sensitive magnetoreception in migratory birds triggered by flavin adenine dinucleotide (FAD) light absorption. A recent study, however, calls into question the ability of vertebrate cryptochrome proteins to bind FAD, rendering them unlikely to function as magnetoreceptive proteins. In this Letter, we investigate the structural changes occurring in Drosophila melanogaster cryptochrome, upon key amino acid mutations, which reduce FAD binding. Through computational analysis we have now suggested why some mutations do not preclude FAD binding in all vertebrate cryptochrome proteins.
Collapse
Affiliation(s)
- Emil Sjulstok
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University, Carl von Ossietzky str. 9-11, 26111 Oldenburg, Germany
| |
Collapse
|