From f6fc92731f4cb873b9d044312c49e8ab44452f0c Mon Sep 17 00:00:00 2001 From: Chelsea Brown Date: Tue, 3 Sep 2024 16:46:02 +0200 Subject: [PATCH 1/5] Added Publications Added two recent publications and removed one --- .DS_Store | Bin 0 -> 6148 bytes docs/.DS_Store | Bin 6148 -> 6148 bytes docs/publications/.DS_Store | Bin 8196 -> 8196 bytes docs/publications/entries/.DS_Store | Bin 24580 -> 24580 bytes ...Chiariello2024_CofactorsPhotosynthesis.qmd | 33 ++++++++++++++++++ .../entries/2024/Korshunova2024_OliGomers.qmd | 33 ++++++++++++++++++ .../entries/2024/Vilach\303\2432024_ROS1.qmd" | 31 ---------------- 7 files changed, 66 insertions(+), 31 deletions(-) create mode 100644 .DS_Store create mode 100644 docs/publications/entries/2024/Chiariello2024_CofactorsPhotosynthesis.qmd create mode 100644 docs/publications/entries/2024/Korshunova2024_OliGomers.qmd delete mode 100644 "docs/publications/entries/2024/Vilach\303\2432024_ROS1.qmd" diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..59805a37fc37e3c9607aef4e687ab25188ef7e3c GIT binary patch literal 6148 zcmeHK%}T>S5Z-O0CKMqD6^{#E3)WV|;w8lT0!H+pQWH}&7_+5m&7l->)EDwmd>&_Z zH)1ho5jz9B-~8@oKgj+t#<)L=4;XV9V>UEIj!KQ7yEfD?$%q`sh>Cn1r7{Bh-NgPn z;I~^WW|G~r{QLJu<21>qoz4euG_AGu4coR`_HFPei(nc~XSp9vuF<-XGL0%dj4qQ= zF?6?1Wi}0yY&1~?Nj!p-o2w*?W#P+N7U!xq&;i?VoT0ljpZD9Md)!;J#k}9`w8dfX zXt8kY?Y;ez^WjtaoXJ;BCkM8bY#OZK4V16dyabahmDvOMs{AUCkQg8ahyh|?l^HOn zg56qW5@_wj05MR@0PYV08lq>g)Tp)&=bTkFH`%-UoIhw z7$64z83WuJ1Op!yWzNAfPW@0>Hq1WLE`sT%Znlp21Qhj)Hzw Q4oDXPMF@4oz%MZH32K~4<^TWy literal 0 HcmV?d00001 diff --git a/docs/.DS_Store b/docs/.DS_Store index 3fc77318fe905a4eae854dcce5fdd23b33d55f49..0ed134352dac928f1573dacb0916655a0ec76523 100644 GIT binary patch delta 23 ecmZoMXffEZf`!deN5RO#c=CEy>CGoutc3ws=m#AD delta 23 ecmZoMXffEZf`!doN5Rn0a`Jjs>CGoutc3wstp^zZ diff --git a/docs/publications/.DS_Store b/docs/publications/.DS_Store index 28610f93371d992bba9d1baec9335390dc241980..f513aab3223ca544479698c2db4b066fd6e62d90 100644 GIT binary patch delta 19 acmZp1XmQvuPk_x*N5RO#c=Hm01bzTN(go!J delta 19 acmZp1XmQvuPk_x_N5Rn0a`O^_1bzTNrv>2v diff --git a/docs/publications/entries/.DS_Store b/docs/publications/entries/.DS_Store index 5bf59e5ee2723e2af9cf1ce9fc3d882895841fc3..97704475a97c91fce05952628b809b85344cd375 100644 GIT binary patch delta 25 hcmZoUz}RwtaYK#_o28C|k%jT(i*~M?x6AlC0|0f<2 ` symbol before the citation, it gives it additional styling. +--> + +## Citation (APA 7) + +> Chiariello, M. G., Zarmiento-Garcia, R., & Marrink, S. J. (2024). Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis. International Journal of Molecular Sciences, 25(14), 7947. + +## Abstract + +As a critical step in advancing the simulation of photosynthetic complexes, we present the Martini 3 coarse-grained (CG) models of key cofactors associated with light harvesting (LHCII) proteins and the photosystem II (PSII) core complex. Our work focuses on the parametrization of beta-carotene, plastoquinone/quinol, violaxanthin, lutein, neoxanthin, chlorophyll A, chlorophyll B, and heme. We derived the CG parameters to match the all-atom reference simulations, while structural and thermodynamic properties of the cofactors were compared to experimental values when available. To further assess the reliability of the parameterization, we tested the behavior of these cofactors within their physiological environments, specifically in a lipid bilayer and bound to photosynthetic complexes. The results demonstrate that our CG models maintain the essential features required for realistic simulations. This work lays the groundwork for detailed simulations of the PSII-LHCII super-complex, providing a robust parameter set for future studies. \ No newline at end of file diff --git a/docs/publications/entries/2024/Korshunova2024_OliGomers.qmd b/docs/publications/entries/2024/Korshunova2024_OliGomers.qmd new file mode 100644 index 00000000..68b6958b --- /dev/null +++ b/docs/publications/entries/2024/Korshunova2024_OliGomers.qmd @@ -0,0 +1,33 @@ +--- +title: "Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS" # Paper title (required) +type: "article" # do not change +sidebar: false # do not change +toc: false # do not change +author: "Ksenia Korshunova, Julius Kiuru, Juho Liekkinen, Giray Enkavi, Ilpo Vattulainen and Bart M. H. Bruininks" # Paper authors (required) +year: "2024" # Publication year (required) +publication: "Journal of Chemical Theory and Computation" # Journal or similar (required) +preprint: "" # URL to prepint page (optional) +doi: "https://doi.org/10.1021/acs.jctc.4c00677" # URL of DOI (required) +materials: "https://pubs.acs.org/doi/10.1021/acs.jctc.4c00677?goto=supporting-info" # URL to suplementary info (optional) +categories: # (required) these keywords will create tags for further filtering. + - Journal article + - Forcefield + - Proteins + - Self-assembly +--- + + + +## Citation (APA 7) + +> Korshunova, K., Kiuru, J., Liekkinen, J., Enkavi, G., Vattulainen, I., & Bruininks, B. M. (2024). Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS. Journal of Chemical Theory and Computation. + +## Abstract + +Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular simulations. It can be combined with a Go̅ model to realistically describe higher-order protein structures while allowing the folding and unfolding events. However, as of today, this method has largely been used only for individual monomers. In this article, we describe how the Go̅ model can be implemented within the framework of Martini 3 for a multimer system, taking into account both intramolecular and intermolecular interactions in an oligomeric protein system. We demonstrate the method by showing how it can be applied to both structural stability maintenance and assembly/disassembly of protein oligomers, using aquaporin tetramer, insulin dimer, and amyloid-β fibril as examples. We find that addition of intermolecular Go̅ potentials stabilizes the quaternary structure of proteins. The strength of the Go̅ potentials can be tuned so that the internal fluctuations of proteins match the behavior of atomistic simulation models, however, the results also show that the use of too strong intermolecular Go̅ potentials weakens the chemical specificity of oligomerization. The Martini-Go̅ model presented here enables the use of Go̅ potentials in oligomeric molecular systems in a computationally efficient and parallelizable manner, especially in the case of homopolymers, where the number of identical protein monomers is high. This paves the way for coarse-grained simulations of large protein complexes, such as viral protein capsids and prion fibrils, in complex biological environments. \ No newline at end of file diff --git "a/docs/publications/entries/2024/Vilach\303\2432024_ROS1.qmd" "b/docs/publications/entries/2024/Vilach\303\2432024_ROS1.qmd" deleted file mode 100644 index 3a840b13..00000000 --- "a/docs/publications/entries/2024/Vilach\303\2432024_ROS1.qmd" +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: "Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations" # Paper title (required) -type: "article" # do not change -sidebar: false # do not change -toc: false # do not change -author: "Juliana F Vilachã, Tsjerk A Wassenaar, and Siewert J Marrink" # Paper authors (required) -year: "2024" # Publication year (required) -publication: "Crystals" # Journal or similar (required) -preprint: "" # URL to prepint page (optional) -doi: "https://doi.org/10.3390/cryst14020106" # URL of DOI (required) -materials: "" # URL to suplementary info (optional) -categories: # (required) these keywords will create tags for further filtering. - - Review - - Proteins ---- - - - -## Citation (APA 7) - -> Vilachã, J. F., Wassenaar, T. A., & Marrink, S. J. (2024). Structural Aspects of the ROS1 Kinase Domain and Oncogenic Mutations. Crystals, 14(2), 106. - -## Abstract - -Protein kinases function as pivotal regulators in biological events, governing essential cellular processes through the transfer of phosphate groups from ATP molecules to substrates. Dysregulation of kinase activity is frequently associated with cancer, ocasionally arising from chromosomal translocation events that relocate genes encoding kinases. Fusion proteins resulting from such events, particularly those involving the proto-oncogene tyrosine-protein kinase ROS (ROS1), manifest as constitutively active kinases, emphasizing their role in oncogenesis. Notably, the chromosomal reallocation of the ros1 gene leads to fusion of proteins with the ROS1 kinase domain, implicated in various cancer types. Despite their prevalence, targeted inhibition of these fusion proteins relies on repurposed kinase inhibitors. This review comprehensively surveys experimentally determined ROS1 structures, emphasizing the pivotal role of X-ray crystallography in providing high-quality insights. We delve into the intricate interactions between ROS1 and kinase inhibitors, shedding light on the structural basis for inhibition. Additionally, we explore point mutations identified in patients, employing molecular modeling to elucidate their structural impact on the ROS1 kinase domain. By integrating structural insights with in vitro and in silico data, this review advances our understanding of ROS1 kinase in cancer, offering potential avenues for targeted therapeutic strategies. \ No newline at end of file From e9916d934fe2c1af9522eea6ab7ab4fee1610169 Mon Sep 17 00:00:00 2001 From: Chelsea Brown <96122099+chelsea-brown@users.noreply.github.com> Date: Thu, 5 Sep 2024 14:44:17 +0200 Subject: [PATCH 2/5] Delete .DS_Store --- .DS_Store | Bin 6148 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 59805a37fc37e3c9607aef4e687ab25188ef7e3c..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHK%}T>S5Z-O0CKMqD6^{#E3)WV|;w8lT0!H+pQWH}&7_+5m&7l->)EDwmd>&_Z zH)1ho5jz9B-~8@oKgj+t#<)L=4;XV9V>UEIj!KQ7yEfD?$%q`sh>Cn1r7{Bh-NgPn z;I~^WW|G~r{QLJu<21>qoz4euG_AGu4coR`_HFPei(nc~XSp9vuF<-XGL0%dj4qQ= 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