Search Results - "Wallin, Stefan"

Comparing effects of attractive interactions in crowded systems: nonspecific, hydrophobic, and hydrogen bond interactions by Bazmi, Saman, Wallin, Stefan

“…The equilibrium stability of a protein is determined by its amino acid sequence and the solution conditions, such as temperature, pH and presence of chemical…”
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Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening by Bhattacherjee, Arnab, Wallin, Stefan

“…The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes, including signal…”
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Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions by Bazmi, Saman, Seifi, Bahman, Wallin, Stefan

“…Macromolecular crowding effects on globular proteins, which usually adopt a single stable fold, have been widely studied. However, little is known about…”
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Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study by Staneva, Iskra, Huang, Yongqi, Liu, Zhirong, Wallin, Stefan

“…The unique ability of intrinsically disordered proteins (IDPs) to fold upon binding to partner molecules makes them functionally well-suited for cellular…”
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Binding free energy landscape of domain-peptide interactions by Staneva, Iskra, Wallin, Stefan

“…Peptide recognition domains (PRDs) are ubiquitous protein domains which mediate large numbers of protein interactions in the cell. How these PRDs are able to…”
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Aggregate geometry in amyloid fibril nucleation by Irbäck, Anders, Jónsson, Sigurður Æ, Linnemann, Niels, Linse, Björn, Wallin, Stefan

“…We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The peptides are represented by…”
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Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding by Zarrine-Afsar, Arash, Wallin, Stefan, Neculai, A. Mirela, Neudecker, Philipp, Howell, P. Lynne, Davidson, Alan R, Chan, Hue Sun

“…Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic…”
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Conformational and aggregation properties of the 1–93 fragment of apolipoprotein A‐I by Petrlova, Jitka, Bhattacherjee, Arnab, Boomsma, Wouter, Wallin, Stefan, Lagerstedt, Jens O., Irbäck, Anders

“…Several disease‐linked mutations of apolipoprotein A‐I, the major protein in high‐density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils…”
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Universality and diversity of folding mechanics for three-helix bundle proteins by Yang, Jae Shick, Wallin, Stefan, Shakhnovich, Eugene I

“…In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece…”
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Impact of N-Terminal Domain Conformation and Domain Interactions on RfaH Fold Switching by Seifi, Bahman, Wallin, Stefan

“…RfaH is a two-domain metamorphic protein involved in transcription regulation and translation initiation. To carry out its dual functions, RfaH relies on two…”
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The C‐terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape by Seifi, Bahman, Wallin, Stefan

“…We simulate the folding and fold switching of the C‐terminal domain (CTD) of the transcription factor RfaH using an all‐atom physics‐based model augmented with…”
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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces by Favrin, Giorgio, Irbäck, Anders, Wallin, Stefan

“…A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three‐helix‐bundle protein, a 46‐amino…”
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Crowding-induced protein destabilization in the absence of soft attractions by Bazmi, Saman, Wallin, Stefan

“…It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft…”
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Three-Helix-Bundle Protein in a Ramachandran Model by Irbäck, Anders, Sjunnesson, Fredrik, Wallin, Stefan

“…We study the thermodynamic behavior of a model protein with 54 amino acids that forms a three-helix bundle in its native state. The model contains three types…”
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Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations by Trotter, Daniel, Wallin, Stefan

“…Experiments have compared the folding of proteins with different amino acid sequences but the same basic structure, or fold. Results indicate that folding is…”
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Binding Specificity Profiles from Computational Peptide Screening by Wallin, Stefan

“…The computational peptide screening method is a Monte Carlo-based procedure to systematically characterize the specificity of a peptide-binding site. The…”
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Interplay between Native State Topology and Sequence in Two-State Protein Folding by Wallin, Stefan, Trotter, Daniel

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Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH by Seifi, Bahman, Aina, Adekunle, Wallin, Stefan

“…RfaH is a compact two‐domain bacterial transcription factor that functions both as a regulator of transcription and an enhancer of translation. Underpinning…”
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Variable Resolution in Scale-Resolved Simulations of Turbulence by Carlsson, Magnus, Wallin, Stefan, Girimaji, Sharath

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Folding, Fold Switching and Energy Landscape of Regulatory Protein RfaH by Seifi, Bahman, Aina, Adekunle, Wallin, Stefan

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