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f | 1 | { | f | 1 | { |
2 | "author": "Marco Lamorte", | 2 | "author": "Marco Lamorte", | ||
3 | "author_email": "", | 3 | "author_email": "", | ||
4 | "creator_user_id": "4a62e96a-67ba-4aee-8d04-41d95ae92835", | 4 | "creator_user_id": "4a62e96a-67ba-4aee-8d04-41d95ae92835", | ||
5 | "extras": [], | 5 | "extras": [], | ||
6 | "groups": [], | 6 | "groups": [], | ||
7 | "id": "cc0585cc-c990-4d18-9a0a-86c543611723", | 7 | "id": "cc0585cc-c990-4d18-9a0a-86c543611723", | ||
8 | "isopen": true, | 8 | "isopen": true, | ||
9 | "license_id": "cc-by", | 9 | "license_id": "cc-by", | ||
10 | "license_title": "Creative Commons Attribuzione", | 10 | "license_title": "Creative Commons Attribuzione", | ||
11 | "license_url": "http://www.opendefinition.org/licenses/cc-by", | 11 | "license_url": "http://www.opendefinition.org/licenses/cc-by", | ||
12 | "maintainer": "BDN", | 12 | "maintainer": "BDN", | ||
13 | "maintainer_email": "dynalife-info@area.bo.cnr.it", | 13 | "maintainer_email": "dynalife-info@area.bo.cnr.it", | ||
14 | "metadata_created": "2024-12-18T10:32:53.621267", | 14 | "metadata_created": "2024-12-18T10:32:53.621267", | ||
t | 15 | "metadata_modified": "2025-02-08T15:58:53.071662", | t | 15 | "metadata_modified": "2025-02-09T22:54:12.994333", |
16 | "name": "preprint-with-doi", | 16 | "name": "preprint-with-doi", | ||
17 | "notes": "This dataset contains preprints related to the research | 17 | "notes": "This dataset contains preprints related to the research | ||
18 | activities of the COST Action CA21169. These works represent | 18 | activities of the COST Action CA21169. These works represent | ||
19 | preliminary findings and have been already associated with a DOI on | 19 | preliminary findings and have been already associated with a DOI on | ||
20 | external data repositories for identification purposes. However, it is | 20 | external data repositories for identification purposes. However, it is | ||
21 | important to note that the presence of a DOI does not imply official | 21 | important to note that the presence of a DOI does not imply official | ||
22 | publication, peer review, or guaranteed quality; these preprints are | 22 | publication, peer review, or guaranteed quality; these preprints are | ||
23 | shared to foster collaboration and early access to scientific | 23 | shared to foster collaboration and early access to scientific | ||
24 | insights.\r\n\r\nThe collection spans contributions from all working | 24 | insights.\r\n\r\nThe collection spans contributions from all working | ||
25 | groups (WG1\u2013WG4), reflecting the interdisciplinary and | 25 | groups (WG1\u2013WG4), reflecting the interdisciplinary and | ||
26 | collaborative spirit of the COST Action. Topics include theoretical | 26 | collaborative spirit of the COST Action. Topics include theoretical | ||
27 | modeling, statistical and computational analyses, experimental | 27 | modeling, statistical and computational analyses, experimental | ||
28 | validation, and dissemination of knowledge across diverse domains of | 28 | validation, and dissemination of knowledge across diverse domains of | ||
29 | biological information systems.", | 29 | biological information systems.", | ||
30 | "num_resources": 1, | 30 | "num_resources": 1, | ||
31 | "num_tags": 1, | 31 | "num_tags": 1, | ||
32 | "organization": { | 32 | "organization": { | ||
33 | "approval_status": "approved", | 33 | "approval_status": "approved", | ||
34 | "created": "2024-12-05T14:56:15.392012", | 34 | "created": "2024-12-05T14:56:15.392012", | ||
35 | "description": "", | 35 | "description": "", | ||
36 | "id": "21a208b5-6551-4dcc-a32f-4d2f32266c96", | 36 | "id": "21a208b5-6551-4dcc-a32f-4d2f32266c96", | ||
37 | "image_url": "", | 37 | "image_url": "", | ||
38 | "is_organization": true, | 38 | "is_organization": true, | ||
39 | "name": "dynalife_publications", | 39 | "name": "dynalife_publications", | ||
40 | "state": "active", | 40 | "state": "active", | ||
41 | "title": "DYNALIFE_PUBLICATIONS", | 41 | "title": "DYNALIFE_PUBLICATIONS", | ||
42 | "type": "organization" | 42 | "type": "organization" | ||
43 | }, | 43 | }, | ||
44 | "owner_org": "21a208b5-6551-4dcc-a32f-4d2f32266c96", | 44 | "owner_org": "21a208b5-6551-4dcc-a32f-4d2f32266c96", | ||
45 | "private": false, | 45 | "private": false, | ||
46 | "relationships_as_object": [], | 46 | "relationships_as_object": [], | ||
47 | "relationships_as_subject": [], | 47 | "relationships_as_subject": [], | ||
48 | "resources": [ | 48 | "resources": [ | ||
49 | { | 49 | { | ||
50 | "cache_last_updated": null, | 50 | "cache_last_updated": null, | ||
51 | "cache_url": null, | 51 | "cache_url": null, | ||
52 | "created": "2024-12-18T10:36:38.685778", | 52 | "created": "2024-12-18T10:36:38.685778", | ||
53 | "datastore_active": false, | 53 | "datastore_active": false, | ||
54 | "description": "**Title:** Molecular Dynamics Simulations Unveil | 54 | "description": "**Title:** Molecular Dynamics Simulations Unveil | ||
55 | the Aggregation Patterns and Salting Out of Polyarginines at | 55 | the Aggregation Patterns and Salting Out of Polyarginines at | ||
56 | Zwitterionic POPC Bilayers in Solutions of Various Ionic | 56 | Zwitterionic POPC Bilayers in Solutions of Various Ionic | ||
57 | Strengths.\r\n\r\n\r\n**Open access:** Yes\r\n\r\n\r\n**Working | 57 | Strengths.\r\n\r\n\r\n**Open access:** Yes\r\n\r\n\r\n**Working | ||
58 | group:** WG2\r\n\r\n\r\n**Resource Type:** DOI provided | 58 | group:** WG2\r\n\r\n\r\n**Resource Type:** DOI provided | ||
59 | preprint.\r\n\r\n\r\n**Resource Format:** | 59 | preprint.\r\n\r\n\r\n**Resource Format:** | ||
60 | PDF\r\n\r\n\r\n**Author(s):** Man Nguyen Thi Hong, Mario | 60 | PDF\r\n\r\n\r\n**Author(s):** Man Nguyen Thi Hong, Mario | ||
61 | Vazdar.\r\n\r\n\r\n**Description/Abstract:** This study employs | 61 | Vazdar.\r\n\r\n\r\n**Description/Abstract:** This study employs | ||
62 | molecular dynamics (MD) simulations to investigate the adsorption and | 62 | molecular dynamics (MD) simulations to investigate the adsorption and | ||
63 | aggregation behavior of simple polyarginine cell-penetrating peptides | 63 | aggregation behavior of simple polyarginine cell-penetrating peptides | ||
64 | (CPPs), specifically modeled as R9 peptides, at zwitterionic | 64 | (CPPs), specifically modeled as R9 peptides, at zwitterionic | ||
65 | phosphocholine POPC membranes under varying ionic strengths of two | 65 | phosphocholine POPC membranes under varying ionic strengths of two | ||
66 | peptide concentrations and two concentrations of NaCl and CaCl2. The | 66 | peptide concentrations and two concentrations of NaCl and CaCl2. The | ||
67 | results reveal an intriguing phenomenon of R9 aggregation at the | 67 | results reveal an intriguing phenomenon of R9 aggregation at the | ||
68 | membrane, which is dependent on the ionic strength indicating a | 68 | membrane, which is dependent on the ionic strength indicating a | ||
69 | salting-out effect. As the peptide concentration and ionic strength | 69 | salting-out effect. As the peptide concentration and ionic strength | ||
70 | increase, peptide aggregation also increases, with aggregate lifetimes | 70 | increase, peptide aggregation also increases, with aggregate lifetimes | ||
71 | and sizes showing a corresponding rise, accompanied by the total | 71 | and sizes showing a corresponding rise, accompanied by the total | ||
72 | decrease of adsorbed peptides at the membrane surface. Notably, in | 72 | decrease of adsorbed peptides at the membrane surface. Notably, in | ||
73 | high ionic strength environments, large R9 aggregates, such as | 73 | high ionic strength environments, large R9 aggregates, such as | ||
74 | octamers, are also observed occasionally. The salting-out, typically | 74 | octamers, are also observed occasionally. The salting-out, typically | ||
75 | uncommon for short positively charged peptides, is attributed to the | 75 | uncommon for short positively charged peptides, is attributed to the | ||
76 | unique properties of arginine amino acid, specifically by its side | 76 | unique properties of arginine amino acid, specifically by its side | ||
77 | chain containing amphiphilic guanidinium (Gdm+) ion which makes both | 77 | chain containing amphiphilic guanidinium (Gdm+) ion which makes both | ||
78 | intermolecular hydrophobic like-charge Gdm+ \u2013 Gdm+ and | 78 | intermolecular hydrophobic like-charge Gdm+ \u2013 Gdm+ and | ||
79 | salt-bridge Gdm+ \u2013 C-terminus interactions, where the former are | 79 | salt-bridge Gdm+ \u2013 C-terminus interactions, where the former are | ||
80 | increased with the ionic strength, and the latter decreased due to | 80 | increased with the ionic strength, and the latter decreased due to | ||
81 | electrostatic screening. The aggregation behavior of R9 peptides at | 81 | electrostatic screening. The aggregation behavior of R9 peptides at | ||
82 | membranes can also linked to their CPP translocation properties, | 82 | membranes can also linked to their CPP translocation properties, | ||
83 | suggesting that aggregation may aid in translocation across cellular | 83 | suggesting that aggregation may aid in translocation across cellular | ||
84 | membranes.\r\n\r\n\r\n**Keywords:**\r\n\r\n\r\n**Affiliation(s):** | 84 | membranes.\r\n\r\n\r\n**Keywords:**\r\n\r\n\r\n**Affiliation(s):** | ||
85 | Institute of Organic Chemistry and Biochemistry of the Czech Academy | 85 | Institute of Organic Chemistry and Biochemistry of the Czech Academy | ||
86 | of Sciences, Prague, Czech Republic. Department of Mathematics, | 86 | of Sciences, Prague, Czech Republic. Department of Mathematics, | ||
87 | Informatics, and Cybernetics, University of Chemistry and Technology, | 87 | Informatics, and Cybernetics, University of Chemistry and Technology, | ||
88 | Prague, Czech Republic.\r\n\r\n\r\n**Publication/Creation Date:** | 88 | Prague, Czech Republic.\r\n\r\n\r\n**Publication/Creation Date:** | ||
89 | April 24, 2024.\r\n", | 89 | April 24, 2024.\r\n", | ||
90 | "format": "HTML", | 90 | "format": "HTML", | ||
91 | "hash": "", | 91 | "hash": "", | ||
92 | "id": "0d79a769-f3e9-4e20-9bb8-1de225977f0b", | 92 | "id": "0d79a769-f3e9-4e20-9bb8-1de225977f0b", | ||
93 | "last_modified": null, | 93 | "last_modified": null, | ||
94 | "metadata_modified": "2024-12-18T10:36:38.822626", | 94 | "metadata_modified": "2024-12-18T10:36:38.822626", | ||
95 | "mimetype": null, | 95 | "mimetype": null, | ||
96 | "mimetype_inner": null, | 96 | "mimetype_inner": null, | ||
97 | "name": "2024_Man Nguyen Thi Hong", | 97 | "name": "2024_Man Nguyen Thi Hong", | ||
98 | "package_id": "cc0585cc-c990-4d18-9a0a-86c543611723", | 98 | "package_id": "cc0585cc-c990-4d18-9a0a-86c543611723", | ||
99 | "position": 0, | 99 | "position": 0, | ||
100 | "resource_type": null, | 100 | "resource_type": null, | ||
101 | "size": null, | 101 | "size": null, | ||
102 | "state": "active", | 102 | "state": "active", | ||
103 | "url": "https://doi.org/10.1101/2024.04.24.590968", | 103 | "url": "https://doi.org/10.1101/2024.04.24.590968", | ||
104 | "url_type": null | 104 | "url_type": null | ||
105 | } | 105 | } | ||
106 | ], | 106 | ], | ||
107 | "state": "active", | 107 | "state": "active", | ||
108 | "tags": [ | 108 | "tags": [ | ||
109 | { | 109 | { | ||
110 | "display_name": "PREPRINT", | 110 | "display_name": "PREPRINT", | ||
111 | "id": "726095c5-5900-4220-96de-d6ff2a88bbe1", | 111 | "id": "726095c5-5900-4220-96de-d6ff2a88bbe1", | ||
112 | "name": "PREPRINT", | 112 | "name": "PREPRINT", | ||
113 | "state": "active", | 113 | "state": "active", | ||
114 | "vocabulary_id": null | 114 | "vocabulary_id": null | ||
115 | } | 115 | } | ||
116 | ], | 116 | ], | ||
117 | "title": "PREPRINTS WITH DOI", | 117 | "title": "PREPRINTS WITH DOI", | ||
118 | "type": "dataset", | 118 | "type": "dataset", | ||
119 | "url": "", | 119 | "url": "", | ||
120 | "version": "" | 120 | "version": "" | ||
121 | } | 121 | } |