Hybrid computational methods combining experimental information with molecular dynamics

A Mondal, S Lenz, JL MacCallum, A Perez - Current Opinion in Structural …, 2023 - Elsevier
A goal of structural biology is to understand how macromolecules carry out their biological
roles by identifying their metastable states, mechanisms of action, pathways leading to …

Structural highlights of macromolecular complexes and assemblies

B Vallat, HM Berman - Current Opinion in Structural Biology, 2024 - Elsevier
The structures of macromolecular assemblies have given us deep insights into cellular
processes and have profoundly impacted biological research and drug discovery. We …

[HTML][HTML] Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data

J Trewhella, P Vachette, AH Larsen - IUCrJ, 2024 - journals.iucr.org
Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS)
conference (Traverse City, 2017), an international team of experts undertook a round-robin …

[HTML][HTML] AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering …

E Brookes, M Rocco, P Vachette… - Journal of Applied …, 2023 - scripts.iucr.org
By providing predicted protein structures from nearly all known protein sequences, the
artificial intelligence program AlphaFold (AF) is having a major impact on structural biology …

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

JB Linse, JS Hub - Communications Chemistry, 2023 - nature.com
Biological macromolecules in solution are surrounded by a hydration shell, whose structure
differs from the structure of bulk solvent. While the importance of the hydration shell for …

[PDF][PDF] Upgraded D22 SEC–SANS setup dedicated to the biology community

A Martel, C Cocho, F Caporaletti… - Journal of applied …, 2023 - journals.iucr.org
Described here is the current status of the upgraded in situ size-exclusion chromatography
(SEC) system implemented with the D22 small-angle neutron scattering (SANS) instrument …

[PDF][PDF] 2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data

J Trewhella, CM Jeffries, AE Whitten - … Crystallographica Section D …, 2023 - journals.iucr.org
In 2017, guidelines were published for reporting structural modelling of small-angle
scattering (SAS) data from biomolecules in solution that exemplified best-practice …

Dynamic Implications of Noncovalent Interactions in Amphiphilic Single-Chain Polymer Nanoparticles

PA Dykeman-Bermingham, LR Stingaciu, C Do… - ACS Macro …, 2024 - ACS Publications
Single-chain polymer nanoparticles (SCNPs) combine the chemical diversity of synthetic
polymers with the intricate structure of biopolymers, generating versatile biomimetic …

Revisiting the use of dioxane as a reference compound for determination of the hydrodynamic radius of proteins by pulsed field gradient NMR spectroscopy

EE Tranchant, F Pesce, NL Jacobsen, CB Fernandes… - bioRxiv, 2023 - biorxiv.org
Measuring the compaction of a protein or complex is key to understand the interactions
within and between biomolecules. Experimentally, protein compaction is often probed either …

Experimental Evidence for the Role of Dynamics in pH-Dependent Enzymatic Activity

Z Wang, S Zhang, Q Xu, Z Li, X Gu… - The Journal of …, 2024 - ACS Publications
Enzymatic activity is heavily influenced by pH, but the rationale for the dynamical
mechanism of pH-dependent enzymatic activity has not been fully understood. In this work …