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Article ; Online: The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach.

Broz, Matic / Oostenbrink, Chris / Bren, Urban

Journal of chemical information and modeling

2024 Volume 64, Issue 6, Page(s) 2077–2083

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 ... ...

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.
MeSH term(s)	Molecular Dynamics Simulation ; Microwaves ; Protein Conformation ; Protein Folding ; Solvents
Chemical Substances	Solvents
Language	English
Publishing date	2024-03-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01937
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Article ; Online: Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.

Broz, Matic / Jukič, Marko / Bren, Urban

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 20

Abstract: Protein structure prediction represents a significant challenge in the field of bioinformatics, with the prediction of protein structures using backbone dihedral angles recently achieving significant progress due to the rise of deep neural network ... ...

Abstract	Protein structure prediction represents a significant challenge in the field of bioinformatics, with the prediction of protein structures using backbone dihedral angles recently achieving significant progress due to the rise of deep neural network research. However, there is a trend in protein structure prediction research to employ increasingly complex neural networks and contributions from multiple models. This study, on the other hand, explores how a single model transparently behaves using sequence data only and what can be expected from the predicted angles. To this end, the current paper presents data acquisition, deep learning model definition, and training toward the final protein backbone angle prediction. The method applies a simple fully connected neural network (FCNN) model that takes only the primary structure of the protein with a sliding window of size 21 as input to predict protein backbone ϕ and ψ dihedral angles. Despite its simplicity, the model shows surprising accuracy for the ϕ angle prediction and somewhat lower accuracy for the ψ angle prediction. Moreover, this study demonstrates that protein secondary structure prediction is also possible with simple neural networks that take in only the protein amino-acid residue sequence, but more complex models are required for higher accuracies.
MeSH term(s)	Deep Learning ; Proteins/chemistry ; Amino Acid Sequence ; Neural Networks, Computer ; Protein Structure, Secondary
Chemical Substances	Proteins
Language	English
Publishing date	2023-10-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28207046
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Article ; Online: Neuropilin (NRPs) Related Pathological Conditions and Their Modulators.

Broz, Matic / Kolarič, Anja / Jukič, Marko / Bren, Urban

International journal of molecular sciences

2022 Volume 23, Issue 15

Abstract: Neuropilin 1 (NRP1) represents one of the two homologous neuropilins (NRP, splice variants of neuropilin 2 are the other) found in all vertebrates. It forms a transmembrane glycoprotein distributed in many human body tissues as a (co)receptor for a ... ...

Abstract	Neuropilin 1 (NRP1) represents one of the two homologous neuropilins (NRP, splice variants of neuropilin 2 are the other) found in all vertebrates. It forms a transmembrane glycoprotein distributed in many human body tissues as a (co)receptor for a variety of different ligands. In addition to its physiological role, it is also associated with various pathological conditions. Recently, NRP1 has been discovered as a coreceptor for the SARS-CoV-2 viral entry, along with ACE2, and has thus become one of the COVID-19 research foci. However, in addition to COVID-19, the current review also summarises its other pathological roles and its involvement in clinical diseases like cancer and neuropathic pain. We also discuss the diversity of native NRP ligands and perform a joint analysis. Last but not least, we review the therapeutic roles of NRP1 and introduce a series of NRP1 modulators, which are typical peptidomimetics or other small molecule antagonists, to provide the medicinal chemistry community with a state-of-the-art overview of neuropilin modulator design and NRP1 druggability assessment.
MeSH term(s)	Animals ; COVID-19 ; Humans ; Neoplasms ; Neuropilin-1/chemistry ; Neuropilin-1/genetics ; Neuropilin-2/genetics ; SARS-CoV-2
Chemical Substances	Neuropilin-2 ; Neuropilin-1 (144713-63-3)
Language	English
Publishing date	2022-07-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23158402
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Book ; Thesis: Eltern im Kinderkrankenhaus

Broz, Michael

Motive der Eltern für ihre Mitaufnahme

1992

Author's details	vorgelegt von Michael Broz
Language	German
Size	91 S. : graph. Darst.
Document type	Book ; Thesis
Thesis / German Habilitation thesis	München, Univ., Diss., 1993
HBZ-ID	HT006367167
Database	Catalogue ZB MED Medicine, Health

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94 D 3041	order for loan	Magazin

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Article: The Effect of the Ala16Val Mutation on the Secondary Structure of the Manganese Superoxide Dismutase Mitochondrial Targeting Sequence.

Broz, Matic / Furlan, Veronika / Lešnik, Samo / Jukič, Marko / Bren, Urban

Antioxidants (Basel, Switzerland)

2022 Volume 11, Issue 12

Abstract: Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine ...

Abstract	Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine to valine (Ala16Val) in the primary structure of immature MnSOD, has been associated with several types of cancer and other autoimmune diseases. However, no conclusive correlation has been established yet. This study aims to determine the effect of the alanine to valine mutation on the secondary structure of the MnSOD mitochondrial targeting sequence (MTS). A model for each variant of the MTS was prepared and extensively simulated with molecular dynamics simulations using the CHARMM36m force field. The results indicate that the alanine variant of the MTS preserves a uniform α-helical secondary structure favorable for the protein transport into mitochondria, whereas the valine variant quickly breaks down its α-helix. Thus, the alanine MTS represents the more active MnSOD variant, the benefits of which have yet to be determined experimentally.
Language	English
Publishing date	2022-11-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704216-9
ISSN	2076-3921
ISSN	2076-3921
DOI	10.3390/antiox11122348
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Article ; Online: The Effect of the Ala16Val Mutation on the Secondary Structure of the Manganese Superoxide Dismutase Mitochondrial Targeting Sequence

Broz, Matic / Furlan, Veronika / Lešnik, Samo / Jukić, Marko / Bren, Urban

Antioxidants. 2022 Nov. 27, v. 11, no. 12

2022

Abstract	Manganese Superoxide Dismutase (MnSOD) represents a mitochondrial protein that scavenges reactive oxygen species (ROS) responsible for oxidative stress. A known single nucleotide polymorphism (SNP) rs4880 on the SOD2 gene, causing a mutation from alanine to valine (Ala16Val) in the primary structure of immature MnSOD, has been associated with several types of cancer and other autoimmune diseases. However, no conclusive correlation has been established yet. This study aims to determine the effect of the alanine to valine mutation on the secondary structure of the MnSOD mitochondrial targeting sequence (MTS). A model for each variant of the MTS was prepared and extensively simulated with molecular dynamics simulations using the CHARMM36m force field. The results indicate that the alanine variant of the MTS preserves a uniform α-helical secondary structure favorable for the protein transport into mitochondria, whereas the valine variant quickly breaks down its α-helix. Thus, the alanine MTS represents the more active MnSOD variant, the benefits of which have yet to be determined experimentally.
Keywords	alanine ; genes ; mitochondria ; mitochondrial proteins ; models ; molecular dynamics ; oxidative stress ; protein transport ; reactive oxygen species ; single nucleotide polymorphism ; superoxide dismutase ; valine
Language	English
Dates of publication	2022-1127
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2704216-9
ISSN	2076-3921
ISSN	2076-3921
DOI	10.3390/antiox11122348
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: 2021 occultations and transits of Linus orbiting (22) Kalliope

Brož, M. / Ďurech, J. / Ferrais, M. / Lee, H. -J. / Kim, M. -J. / Roh, D. -G. / Yim, H. -S. / Jehin, E. / Burdanov, A. / de Wit, J. / Fatka, P. / Hanuš, J. / Carry, B.

I. Polygonal and `cliptracing' algorithm

2023

Abstract: The satellite Linus orbiting the main-belt asteroid (22) Kalliope exhibited occultation and transit events in late 2021. A photometric campaign was organized and observations were taken by the TRAPPIST-South, SPECULOOS-Artemis, OWL-Net, and BOAO ... ...

Abstract	The satellite Linus orbiting the main-belt asteroid (22) Kalliope exhibited occultation and transit events in late 2021. A photometric campaign was organized and observations were taken by the TRAPPIST-South, SPECULOOS-Artemis, OWL-Net, and BOAO telescopes, with the goal to constrain models of this system. Our dynamical model is complex, with multipoles (up to the order $\ell = 2$), internal tides, and external tides. The model was constrained by astrometry (spanning 2001--2021), occultations, adaptive-optics imaging, calibrated photometry, as well as relative photometry. Our photometric model was substantially improved. A new precise (${<}\,0.1\,{\rm mmag}$) light curve algorithm was implemented, based on polygon intersections, which are computed exactly -- by including partial eclipses and partial visibility of polygons. Moreover, we implemented a `cliptracing' algorithm, based again on polygon intersections, in which partial contributions to individual pixels are computed exactly. Both synthetic light curves and synthetic images are then very smooth. Based on our combined solution, we confirmed the size of Linus, $(28\pm 1)\,{\rm km}$. However, this solution exhibits some tension between the light curves and the PISCO speckle-interferometry dataset. In most solutions, Linus is darker than Kalliope, with the albedos $A_{\rm w} = 0.40$ vs. $0.44$. This is confirmed on deconvolved images. A~detailed revision of astrometric data allowed us to revise also the $J_2 \equiv -C_{20}$ value of Kalliope. Most importantly, a~homogeneous body is excluded. For a differentiated body, two solutions exist: low-oblateness ($C_{20} \simeq -0.12$), with a~spherical iron core, and alternatively, high-oblateness ($C_{20} \simeq -0.22$) with an elongated iron core. These correspond to the low- and high-energy collisions, respectively, studied by means of SPH simulations in our previous work. Comment: Astronomy and Astrophysics, accepted
Keywords	Astrophysics - Earth and Planetary Astrophysics ; Astrophysics - Instrumentation and Methods for Astrophysics
Subject code	629
Publishing date	2023-06-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Tazemetostat in the therapy of pediatric INI1-negative malignant rhabdoid tumors.

Vejmelkova, Klara / Pokorna, Petra / Noskova, Kristyna / Faustmannova, Anna / Drabova, Klara / Pavelka, Zdenek / Bajciova, Viera / Broz, Martin / Tinka, Pavel / Jezova, Marta / Palova, Hana / Kren, Leos / Valik, Dalibor / Slaby, Ondrej / Sterba, Jaroslav

Scientific reports

2023 Volume 13, Issue 1, Page(s) 21623

Abstract: Rhabdoid tumors are aggressive tumors that may arise in the kidney, soft tissue, central nervous system, or other organs. They are defined by SMARCB1 (INI1) or SMARCA4 alterations. Often, very young children are affected, and the prognosis is dismal. ... ...

Abstract	Rhabdoid tumors are aggressive tumors that may arise in the kidney, soft tissue, central nervous system, or other organs. They are defined by SMARCB1 (INI1) or SMARCA4 alterations. Often, very young children are affected, and the prognosis is dismal. Four patients with primary atypical teratoid rhabdoid tumor (AT/RT, a rhabdoid tumor in the central nervous system) were treated by resection and high dose chemotherapy. Tazemetostat was introduced after completion of chemotherapy. Three patients have achieved an event free survival of 32, 34, and 30 months respectively. One progressed and died. His overall survival was 20 months. One patient was treated for a relapsed atypical teratoid rhabdoid tumor. The treatment combined metronomic therapy, radiotherapy, tazemetostat and immunotherapy. This patient died of disease progression, with an overall survival of 37 months. One patient was treated for a rhabdoid tumor of the ovary. Tazemetostat was given as maintenance after resection, chemotherapy, and radiotherapy, concomitantly with immunotherapy. Her event free survival is 44 months. Only approximately 40% of patients with rhabdoid tumors achieve long-term survival. Nearly all relapses occur within two years from diagnosis. The event free survival of four of the six patients in our cohort has exceeded this timepoint. Tazemetostat has been mostly tested as a single agent in the relapsed setting. We present promising results when applied as maintenance or add on in the first line treatment.
MeSH term(s)	Humans ; Child ; Female ; Infant ; Child, Preschool ; Rhabdoid Tumor/drug therapy ; Rhabdoid Tumor/pathology ; Neoplasm Recurrence, Local/drug therapy ; SMARCB1 Protein ; Teratoma/pathology ; Central Nervous System Neoplasms/pathology ; DNA Helicases ; Nuclear Proteins ; Transcription Factors
Chemical Substances	tazemetostat (Q40W93WPE1) ; SMARCB1 Protein ; SMARCA4 protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; Nuclear Proteins ; Transcription Factors
Language	English
Publishing date	2023-12-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-48774-2
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Article: Analiza najcesćih uzroka neuspjeha totalnih zubnih proteza.

Broz, M

Vojnosanitetski pregled

1989 Volume 46, Issue 1, Page(s) 32–35

Abstract: The most frequent failures in complete denture construction are examined. All possible failures have been taken into con- been divided into 3 groups: failures in denture retention, in interocclusal relations and factors which are reducing denture ... ...

Title translation	Analysis of the most common causes of failure in complete dentures.
Abstract	The most frequent failures in complete denture construction are examined. All possible failures have been taken into con- been divided into 3 groups: failures in denture retention, in interocclusal relations and factors which are reducing denture stabilization. Failures in the lower complete denture retention with poor extension have been most frequently found (90% cases). Less frequent was poor extension of the upper complete denture. Disbalance such as excentric occlusion and articulation blocking have been frequently found. A sizable vertical occlusal dimension was also significant.
MeSH term(s)	Dental Occlusion ; Denture Retention ; Denture, Complete ; Humans
Language	Serbian
Publishing date	1989-01
Publishing country	Serbia
Document type	English Abstract ; Journal Article
ZDB-ID	123795-0
ISSN	0042-8450
ISSN	0042-8450
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Book ; Online: Observed tidal evolution of Kleopatra's outer satellite

Brož, M. / Ďurech, J. / Carry, B. / Vachier, F. / Marchis, F. / Hanuš, J. / Jorda, L. / Vernazza, P. / Vokrouhlický, D. / Walterová, M. / Behrend, R.

2021

Abstract: The orbit of the outer satellite Alexhelios of (216) Kleopatra is already constrained by adaptive-optics astrometry, obtained with the VLT/SPHERE instrument. However, there is also a preceding occultation event in 1980 attributed to this satellite. ... ...

Abstract	The orbit of the outer satellite Alexhelios of (216) Kleopatra is already constrained by adaptive-optics astrometry, obtained with the VLT/SPHERE instrument. However, there is also a preceding occultation event in 1980 attributed to this satellite. Hereinafter, we try to link all observations, spanning 1980--2018. We find the nominal orbit exhibits an unexplained shift by $+60^\circ$ in the true longitude. Using both periodogram analysis and an $\ell = 10$ multipole model suitable for the motion of mutually interacting moons about the irregular body, we confirmed that it is not possible to adjust the respective osculating period $P_2$. Instead, we were forced to use a model with tidal dissipation (and increasing orbital periods) to explain the shift. We also analyzed light curves, spanning 1977--2021, and searched for the expected spin deceleration of Kleopatra. According to our best-fit model, the observed period rate is $\dot P_2 = (1.8\pm 0.1)\cdot 10^{-8}\,{\rm d}\,{\rm d}^{-1}$ and the corresponding time lag $\Delta t_2 = 42\,{\rm s}$ of tides, for the assumed value of the Love number $k_2 = 0.3$. It is the first detection of tidal evolution for moons orbiting 100-km asteroids. The corresponding dissipation factor $Q$ is comparable with other terrestrial bodies, albeit at a higher loading frequency $2\|\omega-n\|$. We also predict a secular evolution of the inner moon, $\dot P_1 = 5.0\cdot 10^{-8}$, as well as a spin deceleration of Kleopatra, $\dot P_0 = 1.9\cdot 10^{-12}$. In alternative models, with moons captured in the 3:2 mean-motion resonance or more massive moons, the respective values of $\Delta t_2$ are a factor of 2--3 lower. Future astrometric observations by direct imaging or occultations should allow to distinguish between these models, which is important for the internal structure and mechanical properties of (216) Kleopatra. Comment: accepted in A&A
Keywords	Astrophysics - Earth and Planetary Astrophysics
Subject code	551
Publishing date	2021-10-25
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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