Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.Comment: This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright \c{opyright} American Chemical Society after peer review and technical editing by the publishe

Information routing in proteins: the case of a therapeutic antibody

Internal dynamics is the link between structure and biological function in proteins [1]. It has been shown that low-frequency dynamics is not only essential for a protein to function [2], but also that a correlation exists between a protein's activity and its specific dynamical properties [3]. Propagation of information between two or more distant sites on the protein network allows concerted, large-scale conformational changes to take place, triggering as a consequence biological responses.In this work, we aim at identifying patterns of information routing within the therapeutic antibody pembrolizumab [4], as communication channels that emerge from the underlying topology and drive the observed correlated motions. Specifically, we focus on the mutual information (MI) of the displacements of atomic positions, as computed from atomistic molecular dynamics simulations, both in presence and in absence of the bound antigen. MI is used to build network models of the antibody for each of the conformational clusters emerging from the simulations; these networks are then interpreted in the light of a graph-theoretical approach, to couple chemical detail and large-scale dynamics.Unveiling inter-residue communication pathways in may find application not only in biotechnological manipulation for improved therapeutic agents, but also in design of simplified, multi-resolution antibody models that, describing channels of information transfer at an appropriate high-resolution level, facilitate the dynamical investigation at a lower computational cost [5] . [1] Berendsen, H. J., Hayward, S. (2000). Curr. Opin. Struct. Biol., 10(2), 165-169[2] Yang, L. Q., et al. (2014). J. Biomol. Struct. Dyn., 32(3), 372-393.[3] Hensen, U., et al. (2012). PloS one, 7(5), e33931.[4] Scapin, G., et al. (2015). Nat. Struct. Biol., 22(12), 953-958.[5] Diggins IV, P., et al. (2018). J. Chem. Theory Comput., 15(1), 648-664

Just a Flexible Linker? the Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy

Here, we present a structural and dynamic description of CBP-ID4 at atomic resolution. ID4 is the fourth intrinsically disordered linker of CREB-binding protein (CBP). In spite of the largely disordered nature of CBP-ID4, NMR chemical shifts and relaxation measurements show a significant degree of α-helix sampling in the protein regions encompassing residues 2-25 and 101-128 (1852-1875 and 1951-1978 in full-length CBP). Proline residues are uniformly distributed along the polypeptide, except for the two α-helical regions, indicating that they play an active role in modulating the structural features of this CBP fragment. The two helical regions are lacking known functional motifs, suggesting that they represent thus-far uncharacterized functional modules of CBP. This work provides insights into the functions of this protein linker that may exploit its plasticity to modulate the relative orientations of neighboring folded domains of CBP and fine-tune its interactions with a multitude of partners. © 2016 Biophysical Society

Pooled Analysis of Clinical Outcome of Patients with Chemorefractory Metastatic Colorectal Cancer Treated within Phase I/II Clinical Studies Based on Individual Biomarkers of Susceptibility : a Single-Institution Experience

BACKGROUND: Patients with metastatic colorectal cancer (mCRC) refractory to standard therapies have a poor prognosis. In this setting, recruitment into clinical trials is warranted, and studies driven by selection according to individual tumor molecular characteristics are expected to provide added value. OBJECTIVE: We retrospectively analyzed data from patients with mCRC refractory to or following failure of standard therapies who were enrolled into phase I/II clinical studies at the Niguarda Cancer Center based on the presence of a specific molecular profile expected to represent the target of susceptibility to the experimental drug(s). PATIENTS AND METHODS: From June 2011 to May 2016, 2044 patients with mCRC underwent molecular screening. Eighty patients (3.9%) were enrolled in ad hoc studies; the median age was 60 years (range 36-86) and the median number of previous treatment lines was five (range 2-8). Molecular characteristics exploited within these studies were MGMT promoter hypermethylation (48.7%), HER2 amplification (28.8%), BRAF V600E mutation (20%), and novel gene fusions involving ALK or NTRK (2.5%). RESULTS: One patient (1%) had RECIST (Response Evaluation Criteria In Solid Tumors) complete response (CR), 13 patients (16.5%) experienced a partial response (PR), and 28 (35%) stable disease (SD). Median progression-free survival (PFS) was 2.8 months (range 2.63-3.83), with 24% of patients displaying PFS >5 months. Median growth modulation index (GMI) was 0.85 (range 0-15.61) and 32.5% of patients had GMI >1.33. KRAS exon 2 mutations were found in 38.5% of patients, and among the 78 patients with known KRAS status, those with wild-type tumors had longer PFS than those with mutated tumors (3.80 [95% CI 2.80-5.03] vs. 2.13 months [95% CI 1.77-2.87], respectively, p = 0.001). Median overall survival (OS) was 7.83 months (range 7.17-9.33) for all patients, and patients with KRAS wild-type tumors had longer OS than those with mutated tumors (7.83 [95% CI 7.33-10.80] vs. 7.18 months [95% CI 5.63-9.33], respectively, p = 0.06). CONCLUSIONS: This single-institution retrospective study indicates that in a heavily pretreated population approximately 4% of mCRC tumors display a potential actionable molecular context suitable for therapeutic intervention. Application of molecular selection is challenging but improves clinical outcome even in later lines of treatment

Hybrid multiscale simulation scheme to accurately predict binding poses and potency in low-resolution membrane receptors of pharmaceutical relevance

Human G-protein coupled receptors (hGPCRs) are arguably the most pharmaceutically relevant protein superfamily: they are the target of more than 30% of all approved drugs in the US. hGPCRs are alpha-helical proteins embedded in the cellular membrane. A binding site accommodating the ligand is located inside the helix bundle. The rational design of receptor-targeting drugs with high affinity and specificity is impaired, in many cases, by the paucity of structural experimental information and by the low sequence identity between members of the receptors' family. This is the case of at least 50% hGPCRs. Molecular Mechanics/Coarse-Grained (MM/CG) simulations developed in our lab can address this issue by providing accurate ligand binding poses for hGPCR/ligand low-resolution complexes. In this Thesis we implement a method (Open Boundary-Molecular Mechanics/Coarse-Grained, OB-MM/CG) that further expands the scope of the MM/CG approach, by overcoming limitations in describing ligand solvation. In this regard, I coupled a dual-resolution description of the receptor (MM/CG) with an adaptive resolution scheme for the solvent (Hamiltonian adaptive resolution scheme, H-AdResS) developed by Potestio et al. Given that H-AdResS had been previously applied only to homogeneous liquids, I first validated H-AdResS in the context of biological systems, specifically for the description of dual-resolution water solvating atomistic cytoplasmic proteins. The accuracy of the approach is established by reproducing structural and dynamical properties calculated using atomistic simulations. Hence, I next implemented the OB-MM/CG method by coupling hybrid representations of both the protein/ligand complex and the solvent. Comparisons performed on a well-tested receptor/ligand complex with respect to fully atomistic simulations could assess the reliability of the method and the improvement with respect to the previous MM/CG implementation. Importantly, the representation of the solvent leads to the simulation of a well-defined statistical ensemble - the grand canonical one - in the high-resolution region allowing, in principle, calculation of binding affinities. Therefore, my implementation paves the way to rigorous free energy calculations of ligand/protein interactions even for the challenging case of low-resolution protein models