Biology subjects

Tuffery, P.

Publications and source records attributed to Tuffery, P..

6 recordsLinked to original sources

bioRxiv2025

Robust conformational space exploration of cyclic peptides by combining different MD protocols and force fields

Cyclic peptides are an important class of pharmaceutical drugs. We used here replica-exchange molecular dynamics (REMD) and simulated tempering (ST) simulations to explore the conformational landscape of a set of nine cyclic peptides. The N-ter to C-ter backbone cyclized peptides of seven to ten residues were previously designed for a high conformational stability with a mixture of L and D amino acids. Their experimental NMR structures were available in the protein data bank (PDB). For each peptide we tested several force fields, Amber96, Amber14, RSFF2C and Charmm36m in implicit and explicit solvent. We find that the variability of the free energy maps obtained from several protocols is larger than the variability obtained by just repeating the same protocol. Running multiple protocols is therefore important for the convergence assessment of REMD or ST simulations. The majority of the free energy maps showed clusters with a high RMSD to the native structures, revealing the residual flexibility of this set of cyclic peptides. The high RMSD clusters had in some cases the lowest free energy, rendering the prediction of the native structure more difficult with a single protocol. Fortunately, the combination of four implicit solvent REMD and ST simulations, mixing the Amber96 and Am-ber14 force fields, predicted robustly the native structure. As implicit solvent in the REMD or ST setup are up to one hundred times faster than explicit solvent simulations, so running four implicit solvent simulations is a good practical choice. We checked that the use of an explicit solvent REMD or ST simulation, taken alone or combined with implicit solvent simulations, did not significantly improved our results. It results that our combination of four implicit solvent simulations is tied in terms of success rate with much more expensive combinations that include explicit solvent simulations. This may be used as guideline for further studies of cyclic peptide conformations.

biophysics↗

bioRxiv2024

Simulated Solute Tempering 2

Molecular dynamics (MD) simulations are powerful tools for studying the movement and interactions of molecules, but they can be computationally expensive, especially for large biomolecules like proteins. This is problematic because accurately simulating the motions of these molecules is key to understanding their function. Enhanced sampling methods, such as Simulated Tempering (ST), temperature Replica Exchange Molecular Dynamics (REMD) and Replica Exchange with Solute Tempering (REST and REST2), have been developed to overcome this challenge by improving the efficiency of MD simulations. This article presents a new enhanced sampling method called Simulated Solute Tempering 2 (SST2) that builds upon the strengths of ST and REST2. SST2 selectively scales the interactions inside a biomolecule and with its surrounding environment, effectively accelerating the exploration of its different structural states and their stability at various temperatures. SST2 was tested on three different systems (chignolin CLN025, Trp-Cage, and a protein-peptide complex, p97/PNGase) and found to achieve comparable or superior sampling efficiency to ST, SST1 and REST2 while requiring fewer temperature rungs. Notably, SST2 is particularly well-suited for investigating large biomolecular systems, making it a valuable tool for studying a wide range of biomolecular processes, from protein folding to ligand binding. Significance StatementAccurately simulating the motions of biological molecules like proteins is key to understanding their function. However, this is computationally expensive, especially for large systems or slow processes. To overcome this, we developed Simulated Solute Tempering 2 (SST2), a novel algorithm that improves the efficiency of molecular dynamics (MD) simulations. SST2 selectively scales the interactions inside a biomolecule and with its surrounding environment, accelerating the exploration of its different structures and their stability at various temperatures. This allows SST2 to achieve remarkable performances with a clear improved ease of use compare to similar methods, particularly for large systems like protein-ligand complexes. This makes SST2 a valuable tool for studying a wide range of biomolecular processes, from protein folding to ligand binding. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/613476v3_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@761755org.highwire.dtl.DTLVardef@f5df1forg.highwire.dtl.DTLVardef@ba93dorg.highwire.dtl.DTLVardef@193e7eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution

1Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. In this study, we go one step beyond by combining the Debye-Huckel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.

bioinformatics↗

bioRxiv2022

A novel computational method for head-to-tail peptide cyclization: application to urotensin II

Backbone head-to-tail cyclization is one effective strategy to stabilize the conformation of bioactive peptides, preventing enzymatic degradation and improving their bioavailibility. However, very little is known about the requirements to rationally design linkers for the cyclization of linear peptides. Recently, we have shown that large scale data-mining of protein structures can lead to the precise identification of protein loop conformations. Here, we transpose this approach to head-to-tail peptide cyclization. We first show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation improving by over 1 [A] over pre-existing protocols. Secondly, and more importantly, we show that it is possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition. As experimental validation, we first apply our approach to design linkers for the head-to-tail cyclizations of a peptide derived from Nrf2. The designed cyclized peptide shows a 26-fold increase in binding affinity. We then consider urotensin II, a cyclic peptide already stabilized by a disulfide bond, that exerts a broad array of biological activities. The designed head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue shows an excellent retention of in vitro activity. Overall, we propose the first framework for the rational peptide head-to-tail cyclization and reveal its potential for cyclic peptide-based drug design.

bioinformatics↗

bioRxiv2021

Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

The nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear morphology and gene expression. To understand how the Arabidopsis nucleoskeleton physically connects to the nuclear periphery, we investigated the nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. Computational predictions identified three evolutionary conserved peptide motifs within the N-terminal region of KAKU4. Functional analysis revealed that these motifs are required for homomerization of KAKU4, interaction with the nucleoskeleton proteins CROWDED NUCLEI (CRWN) and localization at the nuclear periphery. We find that similar protein motifs are present in NUP82 and NUP136, two plant specific nucleoporins from the Nuclear Pore Complex (NPC) basket. These conserved motifs allow the two nucleoporins to bind CRWN proteins, thus revealing a physical link between the nucleoskeleton and nuclear pores in plants. Finally, whilst NUP82, NUP136 and KAKU4 have a common evolutionary history predating non-vascular land plants, KAKU4 mainly localizes outside the NPC suggesting neofunctionalization of an ancient nucleoporin into a new nucleoskeleton component.

genetics↗

bioRxiv2019

Identification Of Peptides Interfering The LRRK2/PP1 Interaction

Serine/threonine phosphatases are responsible for counteracting the effect of the protein kinases implicated in the development of several pathologies. Here we identified by PEP-scan approach the sequence of a fragment of LRRK2, a Parkinsons disease associated protein, interacting with the phosphatase PP1. The fragment, that is located in a LRRK2 domain of undefined function, was associated in N-terminal to an optimized cell penetrating peptide in order to study their in vitro and in vivo biological activity. From this original sequence, we developed and studied five interfering peptides (IPs) and identified two peptides able to disrupt the LRRK2/PP1 interaction by in vitro competition in anti-LRRK2 immunoprecipitates. Using FITC-labelled peptides, we confirmed the internalization of the peptides in cell lines as well as in and primary human normal and pathological cells. Finally, we have confirmed by ELISA test the association of Mut3DPT-LRRK2-Long and Mut3DPT-LRRK2-Short peptides to purified PP1 protein in a selective manner. The shortest peptides, MuteDPT-LRRK2-5 to 8 with either N or C-terminal deletions are not able neither disrupt the association LRRK2/PP1 nor to associate to purified PP1 protein. The peptides Mut3DPT-LRRK2-Long and Mut3DPT-LRRK2-Short may be new tools to study the role of LRRK2/PP1 interaction in normal and pathological conditions.

molecular biology↗