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Article: Molecular Dynamics Simulations of Macromolecular Crystals.

Cerutti, David S / Case, David A

Wiley interdisciplinary reviews. Computational molecular science

2018 Volume 9, Issue 4

Abstract: The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, ...

Abstract	The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.
Language	English
Publishing date	2018-11-16
Publishing country	United States
Document type	Journal Article
ISSN	1759-0876
ISSN	1759-0876
DOI	10.1002/wcms.1402
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Article ; Online: Correction: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.

Rao, Aditya G / Wiebeler, Christian / Sen, Saumik / Cerutti, David S / Schapiro, Igor

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 21, Page(s) 12494

Abstract: Correction for 'Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2' by Aditya G. Rao et al., Phys. Chem. Chem. Phys., 2021, DOI: 10.1039/d0cp05314g. ...

Abstract	Correction for 'Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2' by Aditya G. Rao et al., Phys. Chem. Chem. Phys., 2021, DOI: 10.1039/d0cp05314g.
Language	English
Publishing date	2021-05-20
Publishing country	England
Document type	Published Erratum
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d1cp90071d
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Article: Short communication: Effects of in-ovo injection of endocrine disruptors and methyltransferase inhibitor on quail growth and egg-laying performances

Cerutti, C. / Leroux, S. / Gourichon, D. / Labrune, Y. / David, I. / Zerjal, T. / Coustham, V. / Devailly, G. / Pitel, F.

Animal. 2022 Mar., v. 16, no. 3

2022

Abstract: Early experiences, including prenatal environment, are known to influence a wide variety of mechanisms involved in the phenotype elaboration. We investigated the effect of the addition of endocrine disruptors or of a methyltransferase inhibitor during ... ...

Abstract	Early experiences, including prenatal environment, are known to influence a wide variety of mechanisms involved in the phenotype elaboration. We investigated the effect of the addition of endocrine disruptors or of a methyltransferase inhibitor during the embryonic development of quails from different genetic backgrounds (four different quail lines) on their growth and egg-laying performances. Fifty-four pairs of parents per line were used and fertilised eggs from each pair were randomly divided into five groups: a control group without any injection, an injected control group treated by injection into the egg of sesame oil, and three groups treated by injection of Genistein, Bisphenol A or 5-Aza-2′-deoxycytidine. All quails were individually weighed at 8, 21, 36 and 78 days. The age at first egg laid and the number of eggs laid were recorded. These analyses revealed a significant impact of the treatment on growth but no influence on the egg-laying traits. All three molecules significantly affected at least one of the analysed growth traits. In conclusion, we showed that the injection of endocrine disruptors or DNA methyltransferase inhibitor into the egg had significant effects on quail development; these effects were specific to each treatment, but no interaction between line and treatment was observed.
Keywords	DNA methyltransferase ; bisphenol A ; eggs ; embryogenesis ; genistein ; oviposition ; phenotype ; quails ; sesame oil
Language	English
Dates of publication	2022-03
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2257920-5
ISSN	1751-732X ; 1751-7311
ISSN (online)	1751-732X
ISSN	1751-7311
DOI	10.1016/j.animal.2022.100464
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Emulator-based Bayesian inference on non-proportional scintillation models by compton-edge probing.

Breitenmoser, David / Cerutti, Francesco / Butterweck, Gernot / Kasprzak, Malgorzata Magdalena / Mayer, Sabine

Nature communications

2023 Volume 14, Issue 1, Page(s) 7790

Abstract: Scintillator detector response modeling has become an essential tool in various research fields such as particle and nuclear physics, astronomy or geophysics. Yet, due to the system complexity and the requirement for accurate electron response ... ...

Abstract	Scintillator detector response modeling has become an essential tool in various research fields such as particle and nuclear physics, astronomy or geophysics. Yet, due to the system complexity and the requirement for accurate electron response measurements, model inference and calibration remains a challenge. Here, we propose Compton edge probing to perform non-proportional scintillation model (NPSM) inference for inorganic scintillators. We use laboratory-based gamma-ray radiation measurements with a NaI(Tl) scintillator to perform Bayesian inference on a NPSM. Further, we apply machine learning to emulate the detector response obtained by Monte Carlo simulations. We show that the proposed methodology successfully constrains the NPSM and hereby quantifies the intrinsic resolution. Moreover, using the trained emulators, we can predict the spectral Compton edge dynamics as a function of the parameterized scintillation mechanisms. The presented framework offers a simple way to infer NPSMs for any inorganic scintillator without the need for additional electron response measurements.
Language	English
Publishing date	2023-11-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42574-y
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Article ; Online: Short communication: Effects of in-ovo injection of endocrine disruptors and methyltransferase inhibitor on quail growth and egg-laying performances.

Cerutti, C / Leroux, S / Gourichon, D / Labrune, Y / David, I / Zerjal, T / Coustham, V / Devailly, G / Pitel, F

Animal : an international journal of animal bioscience

2022 Volume 16, Issue 3, Page(s) 100464

Abstract	Early experiences, including prenatal environment, are known to influence a wide variety of mechanisms involved in the phenotype elaboration. We investigated the effect of the addition of endocrine disruptors or of a methyltransferase inhibitor during the embryonic development of quails from different genetic backgrounds (four different quail lines) on their growth and egg-laying performances. Fifty-four pairs of parents per line were used and fertilised eggs from each pair were randomly divided into five groups: a control group without any injection, an injected control group treated by injection into the egg of sesame oil, and three groups treated by injection of Genistein, Bisphenol A or 5-Aza-2'-deoxycytidine. All quails were individually weighed at 8, 21, 36 and 78 days. The age at first egg laid and the number of eggs laid were recorded. These analyses revealed a significant impact of the treatment on growth but no influence on the egg-laying traits. All three molecules significantly affected at least one of the analysed growth traits. In conclusion, we showed that the injection of endocrine disruptors or DNA methyltransferase inhibitor into the egg had significant effects on quail development; these effects were specific to each treatment, but no interaction between line and treatment was observed.
MeSH term(s)	Animals ; Coturnix ; Endocrine Disruptors ; Methyltransferases ; Ovum ; Quail
Chemical Substances	Endocrine Disruptors ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2022-02-15
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial, Veterinary
ZDB-ID	2257920-5
ISSN	1751-732X ; 1751-7311
ISSN (online)	1751-732X
ISSN	1751-7311
DOI	10.1016/j.animal.2022.100464
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Article ; Online: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.

Rao, Aditya G / Wiebeler, Christian / Sen, Saumik / Cerutti, David S / Schapiro, Igor

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 12, Page(s) 7359–7367

Abstract: Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. ...

Abstract	Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. These photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates.
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Cyanobacteria/chemistry ; Cyanobacteria/metabolism ; Density Functional Theory ; Histidine/chemistry ; Histidine/metabolism ; Models, Molecular ; Molecular Structure ; Protons
Chemical Substances	Bacterial Proteins ; Protons ; Histidine (4QD397987E)
Language	English
Publishing date	2021-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp05314g
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Article ; Online: Cutting Edge: Neutrophil Complement Receptor Signaling Is Required for BAFF-Dependent Humoral Responses in Mice.

Cumpelik, Arun / Cody, Evan / Yu, Samuel Mon-Wei / Grasset, Emilie K / Dominguez-Sola, David / Cerutti, Andrea / Heeger, Peter S

Journal of immunology (Baltimore, Md. : 1950)

2022 Volume 210, Issue 1, Page(s) 19–23

Abstract: ... on neutrophils lowered serum BAFF levels, led to fewer Peyer's patch germinal center B cells, reduced ...

Abstract	T cell-independent (TI) B cell responses to nonprotein Ags involve multiple cues from the innate immune system. Neutrophils express complement receptors and activated neutrophils can release BAFF, but mechanisms effectively linking neutrophil activation to TI B cell responses are incompletely understood. Using germline and conditional knockout mice, we found that TI humoral responses involve alternative pathway complement activation and neutrophil-expressed C3a and C5a receptors (C3aR1/C5aR1) that promote BAFF-dependent B1 cell expansion and TI Ab production. Conditional absence of C3aR1/C5aR1 on neutrophils lowered serum BAFF levels, led to fewer Peyer's patch germinal center B cells, reduced germinal center B cells IgA class-switching, and lowered fecal IgA levels. Together, the results indicate that sequential activation of complement on neutrophils crucially supports humoral TI and mucosal IgA responses through upregulating neutrophil production of BAFF.
MeSH term(s)	Mice ; Animals ; Neutrophils ; B-Lymphocytes ; Complement System Proteins/metabolism ; Mice, Knockout ; Receptors, Complement/metabolism ; Immunoglobulin A
Chemical Substances	Complement System Proteins (9007-36-7) ; Receptors, Complement ; Immunoglobulin A
Language	English
Publishing date	2022-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2200410
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Article ; Online: A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.

Bogetti, Anthony T / Piston, Hannah E / Leung, Jeremy M G / Cabalteja, Chino C / Yang, Darian T / DeGrave, Alex J / Debiec, Karl T / Cerutti, David S / Case, David A / Horne, W Seth / Chong, Lillian T

The Journal of chemical physics

2022 Volume 153, Issue 6, Page(s) 64101

Abstract: We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables ... ...

Abstract	We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous" backbones: chirality-reversed D-α-residues, the C
Language	English
Publishing date	2022-02-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0019054
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Book ; Online: Emulator-based Bayesian Inference on Non-Proportional Scintillation Models by Compton-Edge Probing

Breitenmoser, David / Cerutti, Francesco / Butterweck, Gernot / Kasprzak, Malgorzata Magdalena / Mayer, Sabine

2023

Abstract: Scintillator detector response modelling has become an essential tool in various research fields such as particle and nuclear physics, astronomy or geophysics. Yet, due to the system complexity and the requirement for accurate electron response ... ...

Abstract	Scintillator detector response modelling has become an essential tool in various research fields such as particle and nuclear physics, astronomy or geophysics. Yet, due to the system complexity and the requirement for accurate electron response measurements, model inference and calibration remains a challenge. Here, we propose Compton edge probing to perform non-proportional scintillation model (NPSM) inference for inorganic scintillators. We use laboratory-based gamma-ray radiation measurements with a NaI(Tl) scintillator to perform Bayesian inference on a NPSM. Further, we apply machine learning to emulate the detector response obtained by Monte Carlo simulations. We show that the proposed methodology successfully constrains the NPSM and hereby quantifies the intrinsic resolution. Moreover, using the trained emulators, we can predict the spectral Compton edge dynamics as a function of the parameterized scintillation mechanisms. The presented framework offers a novel way to infer NPSMs for any inorganic scintillator without the need for additional electron response measurements. Comment: Revised manuscript based on single-blind peer-review (second round)
Keywords	Physics - Instrumentation and Detectors ; Astrophysics - Instrumentation and Methods for Astrophysics ; Condensed Matter - Materials Science ; Physics - Computational Physics ; Physics - Data Analysis ; Statistics and Probability
Publishing date	2023-02-11
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Links between the charge model and bonded parameter force constants in biomolecular force fields.

Cerutti, David S / Debiec, Karl T / Case, David A / Chong, Lillian T

The Journal of chemical physics

2017 Volume 147, Issue 16, Page(s) 161730

Abstract: ... of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs ...

Abstract	The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5-19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α-helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA
MeSH term(s)	Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Oligopeptides/chemistry ; Protein Structure, Secondary ; Proteins/chemistry ; Thermodynamics
Chemical Substances	Oligopeptides ; Proteins
Language	English
Publishing date	2017-11-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4985866
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