Biology subjects

Camilloni, C.

Publications and source records attributed to Camilloni, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Calcium-Driven Activation of Gelsolin: Mechanism and the Active-State Ensemble

Gelsolin is a master regulator of the actin cytoskeleton whose activity is controlled by large Ca2+ dependent conformational transitions of its 6 domains (G1-G6). Despite decades of biochemical and cellular studies, the structural basis of activation of the full-length protein remains poorly understood because active gelsolin is highly dynamic and has largely escaped structural characterization. Here, we combine small-angle X-ray scattering, DEER-EPR spectroscopy, and structure-based molecular dynamics simulations to investigate the transition from the compact inactive state to the actin-binding active form. This integrative approach reveals that activation proceeds through a sequential and domain-dependent mechanism, where different regions of the protein respond to Ca2+ with distinct kinetics and conformational trajectories. Rather than converging toward a single active structure, activated gelsolin populates a heterogeneous ensemble of plastic conformations characterized by asymmetric domain arrangements and extensive structural variability. The two major domain triplets (G1-G3 and G4-G6) display markedly different dynamic behaviors, while actin-binding surfaces are exposed according to a defined hierarchy and remain differentially accessible within the active ensemble, suggesting specialized functional roles for different domains during filament engagement. Together, these findings provide a time- and domain-resolved view of gelsolin activation, establish a structural framework for interpreting its diverse biological functions, and offer new opportunities for targeting gelsolin-associated diseases.

biophysics↗

bioRxiv2026

Assessing multi-eGO Predictions of PDZ2-Peptide Binding across Mutations

Accurately predicting how mutations alter protein-peptide binding remains challenging for molecular simulations because both conformational sampling and binding kinetics are computationally demanding. Here, we investigate whether multi-eGO, a hybrid transferable/structure-based atomistic-resolution model previously developed and validated for protein-small molecule interactions, can be transferred to protein-peptide binding without peptide-specific retraining. Using the PDZ2 domain of protein tyrosine phosphatase basophil-like in complex with the peptide EQVTAV as a benchmark, we first show that multi-eGO reproduces the structural dynamics of PDZ2 and the equilibrium binding thermodynamics of the wild-type complex. The model substantially accelerates both binding and unbinding relative to experiment but accurately preserves the resulting equilibrium dissociation constant. We then introduce conservative mutations in PDZ2 and in the peptide and evaluate their effects on binding without repeating the computationally expensive training procedure. Multi-eGO reproduces the experimentally observed changes in equilibrium dissociation constants, with strong agreement across PDZ2 mutants and moderate agreement when the peptide is also mutated. In contrast, the individual association and dissociation rate constants show substantially weaker agreement with experiment. The results indicate that the simplified energy landscape of multi-eGO limits the quantitative prediction of absolute kinetics while preserving thermodynamic information relevant to relative binding affinity. These findings establish multi-eGO as a computationally efficient approach for protein-peptide recognition and for predicting and rank-ordering the effects of conservative mutations on binding affinity.

biochemistry↗

bioRxiv2025

Electric Field-Induced Destabilization and Surface Modulation of Aβ42 Fibrils in Molecular Simulations: Theoretical Implications for DC Stimulation in Alzheimer's Disease

The amyloid-{beta} peptide 42 (A{beta}42) forms fibrillar aggregates that are a hallmark of Alzheimers disease. While recent pharmacologic therapeutic strategies targeting A{beta}42 fibrils and oligomers have shown promising results, safer and more effective approaches are still needed. Non-invasive brain stimulation (NIBS) techniques such as repetitive transcranial magnetic stimulation (rTMS) and transcranial direct current stimulation (tDCS) have been increasingly explored as a possible complementary intervention, but the molecular mechanisms by which static electric fields could influence amyloid aggregation remain poorly understood. Here, we use atomistic molecular dynamics simulations to investigate the effects of static electric fields on A{beta}42 fibrils. We examine the response of an ex vivo fibril structure, with reconstructed N-terminal regions, to increasing field strengths under different structural restraint conditions. Our results show that the electric field perturbs the disordered N-terminal "fuzzy coat," altering its conformational dynamics and reducing its interactions with the fibril core. This reorganization modifies the surface properties of the fibril, potentially impairing secondary nucleation. Additionally, simulations with unrestrained fibril ends reveal increased fluctuations in core residues, particularly near the N-terminus, indicating a destabilizing effect that may hinder fibril elongation. While the field strengths used here exceed those typical of NIBS, our findings provide a molecular-level rationale for how electric fields could modulate fibril propagation and support further experimental investigations under physiologically relevant conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/678267v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@9b6a01org.highwire.dtl.DTLVardef@14ca26forg.highwire.dtl.DTLVardef@3c42ccorg.highwire.dtl.DTLVardef@458b4f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Structural bases for Nuclear Factor 1-X activation and DNA recognition. Prototypic insight into the NFI transcription factor family

Nuclear Factor I (NFI) proteins were first identified in adenovirus DNA replication and later as regulators of gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer and congenital disorders. Within the NFI family, NFI-X is critical for neural stem cell biology, hematopoiesis, muscle development, muscular dystrophies and oncogenesis. Here, we present the first structural characterization of the NFI transcription factor, NFI-X, both alone and bound to its consensus palindromic DNA site. Our analyses reveal a novel, MH1-like fold within NFI-X DNA-binding domain (DBD) and identify crucial structural determinants for activity, such as a Zn{superscript 2} binding site, dimeric assembly, activation mechanism and DNA-binding specificity. Given the >95% sequence identity within the NFI DBDs, our structural data are prototypic for the entire family; a NFI Rosetta Stone that allows decoding a wealth of biochemical and functional data and provides a precise target for drug design in a wider disease context.

biochemistry↗

bioRxiv2024

Pathological PNPase variants with altered RNA binding and degradation activity affect the phenotype of bacterial and human cell models

Human PNPase (hPNPase) is an essential RNA exonuclease located in mitochondria, where it contributes to RNA import from the cytoplasm, degradation of mitochondrial RNA, and R-loop homeostasis. Biallelic mutations in the hPNPase PNPT1 gene cause different genetic diseases, ranging from hereditary hearing loss to Leigh syndrome. In this work, we used an Escherichia coli model we recently developed to test the effects of four pathological PNPT1 mutations associated with diseases of different severity. Moreover, we generated a new human cell model by introducing PNPT1 mutations into 293T cells via CRISPR-Cas editing. Notably, the bacterial cells expressing the different mutant alleles exhibited similar phenotypes consistent with hPNPase loss of function. In contrast, the human cell model responded differently to the two mutations tested, with responses correlating with the severity of the respective pathologies. We interpreted the data derived from both models in the light of the in vitro RNA binding and degradation activity of the purified wild-type and mutated hPNPase variants. We found that all pathogenic mutations tested caused defects in protein assembly and affected the degradation and RNA binding efficiency to varying degrees. However, the severity of the conditions caused by different mutations did not correlate with the catalytic activity of the mutant proteins. Also, we demonstrated that human PNPase, like its bacterial orthologue, is capable of trimming ssDNA and some mutations inhibit such activity.

genetics↗

bioRxiv2024

A conformational fingerprint for amyloidogenic light chains.

Immunoglobulin light chain amyloidosis (AL) and multiple myeloma (MM) both share the overproduction of a clonal light chain (LC). However, while LCs in MM remain soluble in circulation, AL LCs misfold into toxic soluble species and amyloid fibrils that accumulate in organs, leading to distinct clinical manifestations. The significant sequence variability of LCs has hindered understanding of the mechanisms driving LC aggregation. Nevertheless, emerging biochemical properties, including dimer stability, conformational dynamics, and proteolysis susceptibility, distinguish AL LCs from those in MM under native conditions. This study aimed to identify a conformational fingerprint distinguishing AL from MM LCs. Using small-angle X-ray scattering (SAXS) under native conditions, we analyzed four AL and two MM LCs. We observed that AL LCs exhibited a slightly larger radius of gyration and greater deviations from X-ray crystallography-determined or predicted structures, reflecting enhanced conformational dynamics. SAXS data, integrated with molecular dynamics (MD) simulations, revealed a conformational ensemble where LCs adopt multiple states, with variable and constant domains either bent or straight. AL LCs displayed a distinct, low-populated, straight conformation (termed H state), which maximized solvent accessibility at the interface between constant and variable domains. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) experimentally validated this H state. These findings reconcile diverse experimental observations and provide a precise structural target for future drug design efforts.

biophysics↗

bioRxiv2024

Molecular Insights into the Rescue Mechanism of an hERG Activator Against Severe LQT2 Mutations.

BackgroundMutations in the HERG potassium channel are a major cause of long QT syndrome type 2 (LQT2), which can lead to sudden cardiac death. The HERG channel plays a critical role in the repolarization of the myocardial action potential, and loss-of-function mutations prolong cardiac repolarization. MethodsIn this study, we investigated the efficacy and underlying molecular mechanism of ICA-105574, an HERG activator, in shortening the duration of cardiac repolarization in severe LQT2 variants. We characterized the efficacy of ICA-105574 in vivo, using an animal model to assess its ability to shorten the QT interval and in vitro, in cellular models mimicking severe HERG channel mutations (A561V, G628S, and L779P) to evaluate its impact in enhancing IKr current. Additionally, molecular dynamics simulations were used to investigate the molecular mechanism of ICA-105574 action. ResultsIn vivo, ICA-105574 significantly shortened the QT interval. LQT2 mutations drastically reduced IKr amplitude and suppressed tail currents in cellular models. ICA-105574 restored IKr in A561V and G628S. Finally, in silico data showed that ICA-105574 stabilizes a pattern of interactions similar to gain-of-function SQT1 mutations and can reverse the G628S modifications, through an allosteric network linking the binding site to the selectivity filter and the S5P turret helix, thereby restoring its K+ ion permeability. ConclusionsOur results support the development of HERG activators like ICA-105574 as promising pharmacological molecules against some severe LQT2 mutations and suggest that molecular dynamics simulations can be used to test the ability of molecules to modulate HERG function in silico, paving the way for the rational design of new HERG activators.

biophysics↗

bioRxiv2024

A missense mutation in the gene encoding the Mg-chelatase subunit I leads to a viable pale green line with phenotypic features of potential interest for barley breeding programs

The pale green trait, i.e. reduced chlorophyll content, has been shown to increase the efficiency of photosynthesis and biomass accumulation when photosynthetic microorganisms and tobacco plants are cultivated at high densities. Thus, the hus1 barley mutant is defective in photosystem antenna biogenesis, and exhibits a 50% reduction in leaf chlorophyll content. Nevertheless, its agronomical performance under standard field conditions is comparable to that of the wild-type. This supports the notion that crops can decrease their investment in antenna proteins and chlorophyll biosynthesis without detrimental effects on productivity. Here, we assess the effects of reducing leaf chlorophyll content in barley by altering the chlorophyll biosynthesis pathway (CBP). To this end, we have isolated and characterised the pale green barley mutant xan-h.chli-1, which carries a missense mutation in the Xan-h gene for subunit I of Mg-chelatase (HvCHLI), the first enzyme in the CBP. Intriguingly, xan-h.chli-1 is the only known viable homozygous mutant at the Xan-h locus in barley. The Arg298Lys amino-acid substitution in the ATP-binding cleft causes a slight decrease in HvCHLI protein abundance, and a marked reduction in Mg-chelatase activity. Under controlled growth conditions, mutant plants display reduced accumulation of antenna and photosystem core subunits, together with reduced photosystem II yield relative to wild type under moderate illumination, and consistently higher than wild-type levels at high light intensities. Moreover, the reduced content of leaf chlorophyll is associated with a stable reduction in daily transpiration rate, and slight decreases in total biomass accumulation and water-use efficiency. These traits are reminiscent of phenotypic features of wild barley accessions and landraces that thrive under arid climatic conditions. Overall, our findings make the xan-h.chli-1 allelic variant of potential interest for tailoring barley, and other crop plants, for growth in harsh environments.

plant biology↗

bioRxiv2023

The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A

Allosteric cooperativity between ATP and substrates is a prominent characteristic of the cAMP-dependent catalytic subunit of protein kinase A (PKA). Not only this long-range synergistic action is involved in substrate recognition and fidelity, but it is also likely to regulate PKA association with regulatory subunits and other binding partners. To date, a complete understanding of the molecular determinants for this intramolecular mechanism is still lacking. Here, we integrated NMR-restrained molecular dynamics simulations and a Markov State Model to characterize the free energy landscape and conformational transitions of the catalytic subunit of protein kinase A (PKA-C). We found that the apoenzyme populates a broad free energy basin featuring a conformational ensemble of the active state of PKA-C (ground state) and other basins with lower populations (excited states). The first excited state corresponds to a previously characterized inactive state of PKA-C with the C helix swinging outward. The second excited state displays a disrupted hydrophobic packing around the regulatory (R) spine, with a flipped configuration of the F100 and F102 residues at the C-{beta}4 loop. To experimentally validate the second excited state, we mutated F100 into alanine (F100A) and used NMR spectroscopy to characterize the structural response of the kinase to ATP and substrate binding. While the catalytic efficiency of PKA-CF100A with a canonical peptide substrate remains unaltered, this mutation rearranges the C-{beta}4 loop conformation, interrupting the structural coupling of the two lobes and abolishing the allosteric binding cooperativity of the enzyme. The highly conserved C-{beta}4 loop emerges as a pivotal element able to control the synergistic binding between nucleotide and substrate. These results may explain how mutations or insertions near or within this motif affect the function and drug sensitivity in other homologous kinases.

biophysics↗

bioRxiv2022

Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery

Uneven worldwide vaccination coverage against SARS-CoV-2 and emergence of variants escaping immunity call for broadly-effective and easily-deployable therapeutics. We previously described the human single-chain scFv76 antibody, which recognizes SARS-CoV-2 Alfa, Beta, Gamma and Delta variants. We now show that scFv76 also neutralizes infectivity and fusogenic activity of Omicron BA.1 and BA.2 variants. Cryo-EM analysis reveals that scFv76 binds to a well-conserved SARS-CoV-2 spike epitope, providing the structural basis for its broad-spectrum activity. Moreover, we demonstrate that nebulized scFv76 exhibits therapeutic efficacy in a severe hACE2 transgenic mouse model of COVID-19 pneumonia, as shown by body weight and pulmonary viral load data. Counteraction of infection correlates with the inhibition of lung inflammation observed by histopathology and expression of inflammatory cytokines and chemokines. Biomarkers of pulmonary endothelial damage were also significantly reduced in scFv76-treated mice. Altogether the results support the use of nebulized scFv76 for COVID-19 induced by any SARS-CoV-2 variants emerged so far.

microbiology↗

bioRxiv2022

Multi-eGO: an in-silico lens to look into protein aggregation kinetics at atomic resolution

Protein aggregation into amyloid fibrils is the archetype of aberrant biomolecular self-assembly processes, with more than 50 diseases associated that are mostly uncurable. Understanding aggregation mechanisms is thus of fundamental importance and goes in parallel with the characterization of the structures of the transient oligomers formed in the process. Oligomers have been proven elusive to high-resolution structural techniques, while the large sizes and long-time scales typical of aggregation processes have limited, so far, the use of computational methods. To surmount these limitations, we introduce here multi-eGO, an atomistic, hybrid structure-based model, which leveraging on the knowledge of monomers conformational dynamics and of fibril structures, can efficiently capture the essential structural and kinetics aspects of protein aggregation. Multi-eGO molecular dynamics simulations can describe the aggregation kinetics of thousands of monomers. The concentration dependence of the simulated kinetics, as well as the structural features of the resulting fibrils, are in qualitative agreement with in vitro experiments on an amyloidogenic peptide of Transthyretin, a protein responsible for one of the most common cardiac amyloidosis. Multi-eGO simulations allow to observe in time and at atomic resolution the formation of primary nuclei in a sea of transient lower order oligomers, to follow their growth and the subsequent secondary nucleation events, till the maturation of multiple fibrils. Multi-eGO, combined with the many experimental techniques deployed to study protein aggregation, can provide the structural basis needed to advance the design of molecules targeting amyloidogenic diseases. Significance StatementAlzheimers and Parkinsons diseases are uncurable pathologies associated to the aberrant aggregation of specific proteins into amyloid fibrils. Understanding the mechanism leading to protein aggregation, by characterizing the structures of the oligomeric species populated in the process, would have a tremendous impact on the design of therapeutic molecules. We propose that a structure-based approach to molecular dynamics simulations can allow following at high resolution the aggregation kinetics of thousands of monomers. Having shown that simulations can describe the aggregation of a Transthyretin amyloidogenic peptide, we demonstrate how their efficiency allows acquiring a wealth of structural information. We foresee that integrating the latter with the many techniques developed to study protein aggregation will support the design of molecules to modulate amyloidogenesis.

biochemistry↗

bioRxiv2021

A small molecule stabilises the disordered native state of the Alzheimer's Aβ peptide

The stabilisation of native states of proteins is a powerful drug discovery strategy. It is still unclear, however, whether this approach can be applied to intrinsically disordered proteins. Here we report a small molecule that stabilises the native state of the A{beta}42 peptide, an intrinsically disordered protein fragment associated with Alzheimers disease. We show that this stabilisation takes place by a dynamic binding mechanism, in which both the small molecule and the A{beta}42 peptide remain disordered. This disordered binding mechanism involves enthalpically favourable local {pi}-stacking interactions coupled with entropically advantageous global effects. These results indicate that small molecules can stabilise disordered proteins in their native states through transient non-specific interactions that provide enthalpic gain while simultaneously increasing the conformational entropy of the proteins.

biophysics↗

bioRxiv2021

Refinement of α-synuclein ensembles against SAXS data: Comparison of force fields and methods

The inherent flexibility of intrinsically disordered proteins (IDPs) makes it difficult to interpret experimental data using structural models. On the other hand, molecular dynamics simulations of IDPs often suffer from force-field inaccuracies, and long simulations times or enhanced sampling methods are needed to obtain converged ensembles. Here, we apply metainference and Bayesian/Maximum Entropy reweighting approaches to integrate prior knowledge of the system with experimental data, while also dealing with various sources of errors and the inherent conformational heterogeneity of IDPs. We have measured new SAXS data on the protein -synuclein, and integrate this with simulations performed using different force fields. We find that if the force field gives rise to ensembles that are much more compact than what is implied by the SAXS data it is difficult to recover a reasonable ensemble. On the other hand, we show that when the simulated ensemble is reasonable, we can obtain an ensemble that is consistent with the SAXS data, but also with NMR diffusion and paramagnetic relaxation enhancement data.

biophysics↗

bioRxiv2020

A kinetic ensemble of the Alzheimer's Aβ peptide

The discovery that disordered proteins are widespread in the human proteome has prompted the quest for methods to characterize the conformational properties that determine their functional and dysfunctional behaviour. It has become customary to describe these proteins in terms of structural ensembles and free energy landscapes, which offer conformational and thermodynamic insight. However, a current major challenge is to generalize this description to kinetic ensembles, thereby also providing information on transition rates between states. Approaches based on the theory of stochastic processes can be particularly suitable for this purpose. Here, we develop a Markov state model and illustrate its application by determining a kinetic ensemble of the 42-residue form of the amyloid-{beta} peptide (A{beta}42), whose aggregation is associated with Alzheimers disease. Using the Google Compute Engine, we generated 315 s all-atom, explicit solvent molecular dynamics trajectories, validated with experimental data from nuclear magnetic resonance spectroscopy. Using a probabilistic-based definition of conformational states in a neural network approach, we found that A{beta}42 is characterized by inter-state transitions no longer than the microsecond timescale, exhibiting only fully unfolded or short-lived, partially-folded states. We contextualize our findings by performing additional simulations of the oxidized form of A{beta}42. Our results illustrate how the use of kinetic ensembles offers an effective means to provide information about the structure, thermodynamics, and kinetics of disordered proteins towards an understanding of these ubiquitous biomolecules.

biophysics↗

bioRxiv2020

Conformational stability and dynamics in crystals recapitulate protein behaviour in solution

A growing body of evidences has established that in many cases proteins may preserve most of their function and flexibility in a crystalline environment, and several techniques are today capable to detect transiently-populated states of macromolecules in tightly packed lattices. Intriguingly, in the case of amyloidogenic precursors, the presence of these conformations (hidden to conventional crystallographic studies) can be correlated to the pathological fate of the native fold. It remains unclear, however, to which extent these minor conformations reflect the protein behaviour that is more commonly studied in solution. Here, we address this question by investigating some biophysical properties of a prototypical amyloidogenic system, {beta}2-microglobulin ({beta}2m) in solution and in microcrystalline state. By combining NMR chemical shifts with Molecular Dynamics (MD) simulations, we confirmed that conformational dynamics of {beta}2m native state in the crystal lattice is in keeping with what observed in solution. A comparative study of protein stability in solution and in crystallo is then carried out, monitoring the change in protein secondary structure at increasing temperature by Fourier transform infrared (FTIR) spectroscopy. The increased structural order of the crystalline state contributes to provide better resolved spectral components compared to those collected in solution and crucially, the crystalline samples display thermal stabilities in good agreement with the trend observed in solution. Overall, this work shows that protein stability and occurrence of pathological hidden states in crystals parallel their solution counterpart, confirming the interest of crystals as a platform for the biophysical characterisation of processes such as unfolding and aggregation.

biochemistry↗

bioRxiv2020

Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments

Poly-ubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable their molecular recognition by a large number of partners in multiple biological pathways. By using alternative linkage, it is possible to obtain poly-ubiquitin molecules with different dynamical properties. This flexibility is further increased by the possibility to tune the length of poly-ubiquitin chains. Characterizing the dynamics of poly-ubiquitins as a function of their length is thus relevant to understand their biology. Structural characterization of poly-ubiquitin conformational dynamics is challenging both experimentally and computationally due to increasing system size and conformational variability. Here, by developing highly efficient and accurate small-angle X-ray scattering driven Martini coarse-grain simulations, we characterize the dynamics of linear M1-linked di-, tri- and tetra-ubiquitin chains. Our data show that the behavior of the di-ubiquitin subunits is independent of the presence of additional ubiquitin modules. We propose that the conformational space sampled by linear poly-ubiquitins, in general, may follow a simple self-avoiding polymer model. These results, combined with experimental data from small angle X-ray scattering, biophysical techniques and additional simulations show that binding of NEMO, a central regulator in the NF-{kappa}B pathway, to linear poly-ubiquitin obeys a 2:1 (NEMO:poly-ubiquitin) stoichiometry in solution, even in the context of four ubiquitin units. Eventually, we show how the conformational properties of long poly-ubiquitins may modulate the binding with their partners in a length-dependent manner. SignificanceProtein conformational dynamics plays an essential role in molecular recognition mechanisms. The characterization of conformational dynamics is hampered by the conformational averaging of observable in experimental structural biology techniques and by the limitations in the accuracy of computational methods. By developing an efficient and accurate approach to combine small-angle X-ray scattering solution experiments and coarse-grain Martini simulations, we show that the conformational dynamics of linear poly-ubiquitins can be efficiently determined and to rationalize the role of poly-ubiquitin dynamic in the molecular recognition of the UBAN domain upon binding to the signaling regulator NEMO. The analysis of the conformational ensembles allows us to propose a general model of the dynamics of linear poly-ubiquitin chains where they can be described as a self-avoiding polymer with a characteristic length associated with their specific linkage.

biophysics↗

bioRxiv2020

Evolution of an interaction between disordered proteins resulted in increased heterogeneity of the binding transition state

Intrinsically disordered protein (IDP) domains often have multiple binding partners. Little is known regarding molecular changes in the binding mechanism when a new interaction evolves from low to high affinity. Here we compared the degree of native contacts in the transition state of the interaction of two IDP domains, low-affinity ancestral and high-affinity human NCBD and CID. We found that the coupled binding and folding mechanism of the domains is overall similar, but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex while more heterogenous transient interactions, including electrostatic, and an increased disorder characterize the human complex. From an evolutionary perspective, adaptation to new binding partners for IDPs may benefit from this ability to exploit multiple alternative transient interactions while retaining the overall pathway.

biophysics↗

bioRxiv2018

Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data

Small-angle X-ray scattering (SAXS) use in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speed up by using a coarse grain representation of the structure. Here following the work of Niebling, et al. (J. Appl. Cryst., (2014), 47, 1190) we derived the Martini beads form factors for nucleic acids and we implemented them, together with those previously determined for proteins, in the publicly available PLUMED library. We also implemented a hybrid multi-resolution strategy to perform SAXS restrained simulations at atomic resolution by calculating on-the-fly the virtual position of the Martini beads and using them for the calculation of SAXS. The accuracy and efficiency of the method is demonstrated by refining the structure of two protein/nucleic acid complexes. Instrumental for this result is the use of metainference that allows considering and alleviating the approximations at play in our SAXS calculation.

biochemistry↗