Výsledky vyhledávání - "Majda Misini Ignjatović"

Akademický článek

Interplay of halogen bonding and solvation in protein–ligand binding

Autor: Maria Luisa Verteramo, Majda Misini Ignjatović, Rohit Kumar, Sven Wernersson, Vilhelm Ekberg, Johan Wallerstein, Göran Carlström, Veronika Chadimová, Hakon Leffler, Fredrik Zetterberg, Derek T. Logan, Ulf Ryde, Mikael Akke, Ulf J. Nilsson

Publikováno v: iScience, Vol 27, Iss 4, Pp 109636- (2024)

Summary: Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving fo

Externí odkaz: https://doaj.org/article/04a7dad9b6fc435daabaaf102e239b88

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Akademický článek

Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

Autor: Johan Wallerstein, Vilhelm Ekberg, Majda Misini Ignjatović, Rohit Kumar, Octav Caldararu, Kristoffer Peterson, Sven Wernersson, Ulrika Brath, Hakon Leffler, Esko Oksanen, Derek T. Logan, Ulf J. Nilsson, Ulf Ryde, Mikael Akke

Publikováno v: JACS Au, Vol 1, Iss 4, Pp 484-500 (2021)

Externí odkaz: https://doaj.org/article/2981db6db17549c9b3a2c12397786a4f

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Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks

Autor: Vilhelm Ekberg, Marley L. Samways, Majda Misini Ignjatović, Jonathan W. Essex, Ulf Ryde

Publikováno v: ACS Physical Chemistry Au. 2:247-259

Water molecules play important roles in all biochemical processes. Therefore, it is of key importance to obtain information of the structure, dynamics, and thermodynamics of water molecules around proteins. Numerous computational methods have been su

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a2af618188e5af040f20605bbfa5989
https://doi.org/10.1021/acsphyschemau.1c00052

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Entropy–Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C

Autor: Esko Oksanen, Majda Misini Ignjatović, Ulrika Brath, Octav Caldararu, Sven Wernersson, Kristoffer Peterson, Derek T. Logan, Ulf J. Nilsson, Ulf Ryde, Vilhelm Ekberg, Johan Wallerstein, Mikael Akke, Rohit Kumar, Hakon Leffler

Publikováno v: JACS Au
JACS Au 1(4), 484-500 (2021). doi:10.1021/jacsau.0c00094
JACS Au, Vol 1, Iss 4, Pp 484-500 (2021)

JACS Au 1(4), 484-500 (2021). doi:10.1021/jacsau.0c00094
Molecular recognition is fundamental to biological signaling. A central question is how individual interactions between molecular moieties affect the thermodynamics of ligand binding to pr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f862f31eae11a8c886b7c8019ca91b21
https://doi.org/10.1021/jacsau.0c00094

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Interplay between Conformational Entropy and Solvation Entropy in Protein–Ligand Binding

Autor: Esko Oksanen, Olof Stenström, Ulf J. Nilsson, Mikael Akke, Francesco Manzoni, Maria Luisa Verteramo, Majda Misini Ignjatović, Octav Caldararu, Derek T. Logan, Ulf Ryde, Hakon Leffler, Martin A. Olsson

Publikováno v: Journal of the American Chemical Society; 141(5), pp 2012-2026 (2019)

Understanding the driving forces underlying molecular recognition is of fundamental importance in chemistry and biology. The challenge is to unravel the binding thermodynamics into separate contributions and to interpret these in molecular terms. Ent

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c89d9989ebbab23072e6c6b96bd03d6a
https://doi.org/10.1021/jacs.8b11099

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Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

Autor: Majda Misini Ignjatović, Octav Caldararu, Martin A. Olsson, Meiting Wang, Ulf Ryde

Publikováno v: Journal of Computer-Aided Molecular Design. 32:1027-1046

We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd58637ed02a8414cacfe65fff650822
https://doi.org/10.1007/s10822-018-0158-2

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Water structure in solution and crystal molecular dynamics simulations compared to protein crystal structures

Autor: Octav, Caldararu, Majda, Misini Ignjatović, Esko, Oksanen, Ulf, Ryde

Publikováno v: RSC advances. 10(14)

The function of proteins is influenced not only by the atomic structure but also by the detailed structure of the solvent surrounding it. Computational studies of protein structure also critically depend on the water structure around the protein. Her

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::195617f491ef5c20aba70701dbe89882
https://pubmed.ncbi.nlm.nih.gov/35497843

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Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions

Autor: Rohit Kumar, Majda Misini Ignjatović, Kristoffer Peterson, Martin Olsson, Hakon Leffler, Ulf Ryde, Ulf J. Nilsson, Derek T. Logan

Publikováno v: Chemmedchem
ChemMedChem; 14(16), pp 1528-1536 (2019)

Multipolar fluorine–amide interactions with backbone and side‐chain amides have been described as important for protein–ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e1d5a1bbeecbf0f5e3330db0020131e9
https://pubmed.ncbi.nlm.nih.gov/31246331

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Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects

Autor: Kristoffer Peterson, Derek T. Logan, Hakon Leffler, Ulf J. Nilsson, Majda Misini Ignjatović, Rohit Kumar, Ulf Ryde

Publikováno v: 'Organic & Biomolecular Chemistry ', vol: 17, pages: 1081-1089 (2019)

In the β-D-galactopyranoside-binding protein galectin-3, synthetic inhibitors substituted at the 3-position of a thiodigalactoside core cause the formation of an aglycone binding pocket through the displacement of an arginine residue (Arg144) from i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f27d820723efc5f1ba37f401aeab097a
https://pubmed.ncbi.nlm.nih.gov/30632578

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Can MM/GBSA calculations be sped up by system truncation?

Autor: Paulius Mikulskis, Majda Misini Ignjatović, Ulf Ryde, Pär Söderhjelm

Publikováno v: Journal of Computational Chemistry; 39(7), pp 361-372 (2018)

We have studied whether calculations of the binding free energy of small ligands to a protein by the MM/GBSA approach (molecular mechanics combined with generalized Born and surface area solvation) can be sped up by including only a restricted number

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8142ffb0e4fba62dfb76a8c8a5829b7f
https://lup.lub.lu.se/record/dfd63698-d939-4af2-980a-e4831791b444

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