Amanda E. Sandelin

Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations

Efstathia Mantzari, Cajsa K. Malm, Ricky Nencini, Amanda E. Sandelin et autres

KEEVKKEEVKK, representing common natural and engineered linker repeats. Glycine-rich sequences showed slight looping tendencies, whereas proline-containing sequences adopted extended conformations with increased approximate persistence lengths and slower dynamics. Notably, sodium and calcium binding to charged peptides minimally affected rigidity, indicating electrostatics don't …

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Backbone rigidity of disordered protein linkers from synergistic combination of NMR experiments and MD simulations

Efstathia Mantzari, Cajsa K. Malm, Ricky Nencini, Amanda E. Sandelin et autres

Disordered protein linkers are essential for multidomain protein function and engineering, but quantitative methods for their biophysical characterization remain limited. We combined NMR experiments with molecular dynamics simulations to demonstrate that protein backbone 15N spin relaxation times correlates with backbone rigidities in …

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Quality Evaluation Based Simulation Selection (QEBSS) for analysis of conformational ensembles and dynamics of multidomain proteins

Amanda E. Sandelin, Ricky Nencini, Ekrem Yaşar, Satoshi Fudo et autres

Abstract Multidomain proteins containing both folded and intrinsically disordered regions are crucial for biological processes, but characterizing their conformational ensembles and dynamics remains challenging. We introduce the Quality Evaluation Based Simulation Selection (QEBSS) protocol, which combines MD simulations with NMR-derived protein backbone …

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QEBSS: Quality Evaluation Based Simulation Selection for analysis of conformational ensembles and dynamics of multidomain proteins

Amanda E. Sandelin, Ricky Nencini, Ekrem Yaşar, Satoshi Fudo et autres

Multi-domain proteins, comprising both folded and intrinsically disordered regions, play pivotal roles in various biological processes, yet characterizing their conformational ensembles and dynamics presents significant challenges. Here we address this challenge by introducing the Quality Evaluation Based Simulation Selection (QEBSS) protocol that …

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Rapid Interpretation of Protein Backbone Rotation Dynamics Directly from Spin Relaxation Data

Ricky Nencini, Efstathia Mantzari, Amanda E. Sandelin, O. H. Samuli Ollila

High Resolution Image Download MS PowerPoint Slide Besides their structure, dynamics is pivotal for protein functions, particularly for intrinsically disordered proteins (IDPs) that do not fold into a fixed 3D structure. However, the detection of protein dynamics is difficult for IDPs and …

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Rapid interpretation of protein backbone rotation dynamics directly from spin relaxation data

Ricky Nencini, Efstathia Mantzari, Amanda E. Sandelin, O. H. Samuli Ollila

Besides structure, protein dynamics is pivotal for their functions, particularly for intrinsically disordered proteins (IDPs) that do not fold to a fixed 3D structure. Rapid rotations of chemical bonds in proteins can be detected measuring NMR spin relaxation rates, but interpretation of …

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QEBSS: Quality Evaluation Based Simulation Selection for analysis of conformational ensembles and dynamics of multidomain proteins

Amanda E. Sandelin, Ricky Nencini, Ekrem Yaşar, O. H. Samuli Ollila

Abstract Multi-domain proteins, comprising both folded and intrinsically disordered regions, play pivotal roles in various biological processes, yet characterizing their conformational ensembles and dynamics presents significant challenges. Here we introduce the Quality Evaluation Based Simulation Selection (QEBSS) protocol to address this challenge …

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No correlation between carotid intima-media thickness and long-term glycemic control in individuals with type 1 diabetes

Jussi Inkeri, Valma Harjutsalo, Juha Martola, Jukka Putaala et autres

Abstract Aims To determine whether carotid intima-media thickness (CIMT), a surrogate marker of cardiovascular disease (CVD), is associated with long-term blood glucose control in individuals with type 1 diabetes (T1D). Methods We recruited 508 individuals (43.4% men; median age 46.1, IQR 37.8–55.9 …

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A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes

Natalie R. van Zuydam, Emma Ahlqvist, Niina Sandholm, Harshal Deshmukh et autres

Identification of sequence variants robustly associated with predisposition to diabetic kidney disease (DKD) has the potential to provide insights into the pathophysiological mechanisms responsible. We conducted a genome-wide association study (GWAS) of DKD in type 2 diabetes (T2D) using eight complementary dichotomous …

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Short-term oxygen administration restores blunted baroreflex sensitivity in patients with type 1 diabetes

Luciano Bernardi, Milla Rosengård‐Bärlund, Amanda E. Sandelin, Ville‐Petteri Mäkinen et autres

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