[HTML][HTML] Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies

NH Rogoża, MA Krupa, P Krupa, AK Sieradzan - Molecules, 2024 - mdpi.com
Fullerenes, particularly C60, exhibit unique properties that make them promising candidates
for various applications, including drug delivery and nanomedicine. However, their …

Use of restraints from consensus fragments of multiple server models to enhance protein-structure prediction capability of the UNRES force field

MA Mozolewska, P Krupa, B Zaborowski… - Journal of Chemical …, 2016 - ACS Publications
Recently, we developed a new approach to protein-structure prediction, which combines
template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) …

Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization

G Smaldone, R Berisio, N Balasco, S D'Auria… - … et Biophysica Acta (BBA …, 2018 - Elsevier
Abstract Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate
for arginine biosensing in diagnostics. This protein is endowed with unusual structural …

Proline 235 plays a key role in the regulation of the oligomeric states of Thermotoga maritima Arginine Binding Protein

G Smaldone, M Vigorita, A Ruggiero, N Balasco… - … et Biophysica Acta (BBA …, 2016 - Elsevier
Abstract The Arginine Binding Protein isolated from Thermotoga maritima (TmArgBP) is a
protein endowed with several peculiar properties. We have previously shown that TmArgBP …

[HTML][HTML] Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

AG Lipska, SR Seidman, AK Sieradzan… - The Journal of …, 2016 - pubs.aip.org
The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID:
1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain …

[HTML][HTML] Extension of coarse-grained UNRES force field to treat carbon nanotubes

AK Sieradzan, MA Mozolewska - Journal of Molecular Modeling, 2018 - Springer
Carbon nanotubes (CNTs) have recently received considerable attention because of their
possible applications in various branches of nanotechnology. For their cogent application …

[HTML][HTML] The role of C-terminal helix in the conformational transition of an arginine binding protein

V Santhakumar, NM Mascarenhas - Journal of Structural Biology: X, 2022 - Elsevier
The thermotoga maritima arginine binding protein (TmArgBP) is a periplasmic binding
protein that has a short helix at the C-terminal end (CTH), which is swapped between the …

[HTML][HTML] Reoptimized UNRES potential for protein model quality assessment

E Faraggi, P Krupa, MA Mozolewska, A Liwo… - Genes, 2018 - mdpi.com
Ranking protein structure models is an elusive problem in bioinformatics. These models are
evaluated on both the degree of similarity to the native structure and the folding pathway …

The role of C-terminal helix in the conformational transition of an arginine binding protein

NM Mascarenhas, V Santhakumar - Available at SSRN 4183329 - papers.ssrn.com
The thermotoga maritima arginine binding protein (TmArgBP) is a periplasmic binding
protein that has a short helix at the C-terminal end (CTH), which is swapped between the …

[PDF][PDF] INTERNATIONAL MARINE SCIENCE JOURNAL

L do Carmo Silva, AM Barbosa, IP Tannous, TG Santos… - researchgate.net
Fungal infections increased substantially in the last years, becoming a relevant public health
problem. Many of these infections account for high rates of morbidity and mortality. The …