Applications of Computational Methods to Simulations of Protein Dynamics

Nowak, Wiesław

doi:10.1007/978-94-007-6169-8_31-2

Cited by 3 publications

(3 citation statements)

References 354 publications

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“…For some cases, the structures do not change a lot like for Cpd_B conformer a (RMSD of 0.2 Å) leading to the small energy difference of about 2 kcal mol À1 upon optimizing the whole structures. However, depending on the conformer geometry, also larger energy changes (e.g., 16 For a few cases, the dominant part of the conformational energies is the difference between the pure solute (gas-phase) energies like for Cpd_b (m). Further, there are cases, where the conformers differ mainly by solute-water (e.g., GGF (14) and Cpd_B (I)), or water-water interactions (e.g., GGF (4) and Cpd_B (j)).…”

Section: Benchmark Set and The Effects Of Solvationmentioning

confidence: 99%

“…Thereby, the interaction with water molecules is especially important since they occur typically in the aqueous phase, which is also of major importance for living 14 . To understand such biomolecular processes, computational studies became a valuable tool that have already been applied to enlighten, for example, protein folding, protein‐drug interactions, ligand transport phenomena, and ion channel activity 15‐17 . Thereby, many different methods can be chosen from the classes of Wave Function Theory (WFT), Density Functional Theory (DFT), semi‐empirical quantum mechanical (SQM) methods, and Force Fields (FF) that provide different cost–accuracy ratios limiting, for example, the application of highly accurate methods such as coupled cluster with perturbative triples (CCSD(T)) to relatively small molecular structures 18 .…”

Section: Introductionmentioning

confidence: 99%

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Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

Plett,

Grimme,

Hansen

2023

J Comput Chem

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A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas‐phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254–1266], and provide very accurate PNO‐LCCSD(T)‐F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer–water and water–water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86‐D4/def2‐QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta‐)GGAs and hybrid functionals like B97M‐V and B97M‐D with a large basis set reproduce the coupled cluster reference with an MAD below 1 kcal mol . If more efficient methods are required, the composite DFT‐method rSCAN‐3c (MAD of 1.2 kcal mol) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500–1000 atoms are in the focus, the semi‐empirical GFN2‐xTB or the MMFF94 force field (for very large systems) are recommended.

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Section: Benchmark Set and The Effects Of Solvationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

Plett,

Grimme,

Hansen

2023

J Comput Chem

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“…At the molecular level, highly sophisticated simulators can solve biochemical networks (CellDesigner) ( Funahashi et al, 2008 ), reaction-diffusion systems (STEPS) ( Hepburn et al, 2012 ; Chen and de Schutter, 2017 ), protein folding and protein-protein interactions (NAMD) ( Sotomayor, 2015 ; Nowak, 2016 ), and gene regulatory networks (CYTOSCAPE) ( Shannon, 2003 ; Cline et al, 2007 ). Although these modeling types are grounded in biological reality, they require large amounts of heterogeneous data to visualize large-scale biomolecular networks.…”

Section: Introductionmentioning

confidence: 99%

Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation

Masoli

Rizza

Tognolina

et al. 2022

Front. Comput. Neurosci.

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The neuroscientific field benefits from the conjoint evolution of experimental and computational techniques, allowing for the reconstruction and simulation of complex models of neurons and synapses. Chemical synapses are characterized by presynaptic vesicle cycling, neurotransmitter diffusion, and postsynaptic receptor activation, which eventually lead to postsynaptic currents and subsequent membrane potential changes. These mechanisms have been accurately modeled for different synapses and receptor types (AMPA, NMDA, and GABA) of the cerebellar cortical network, allowing simulation of their impact on computation. Of special relevance is short-term synaptic plasticity, which generates spatiotemporal filtering in local microcircuits and controls burst transmission and information flow through the network. Here, we present how data-driven computational models recapitulate the properties of neurotransmission at cerebellar synapses. The simulation of microcircuit models is starting to reveal how diverse synaptic mechanisms shape the spatiotemporal profiles of circuit activity and computation.

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Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity

Khan

Naeem

2023

Journal of Biomolecular Structure and Dynamics

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Applications of Computational Methods to Simulations of Protein Dynamics

Cited by 3 publications

References 354 publications

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules

Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation

Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity

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