Giulia Morra

Italian National Research Council | CNR · Istituto di Chimica del Riconoscimento Molecolare ICRM

Celiac disease (CD) is a chronic and systemic autoimmune disorder that affects preferentially the small intestine of individuals with a genetic predisposition. CD is promoted by the ingestion of gluten, a storage protein contained in the endosperm of the seeds of wheat, barley, rye, and related cereals. Once in the gastrointestinal (GI) tract, glut...

Class A (rhodopsin-like) G protein-coupled receptors (GPCRs) are constitutive phospholipid scramblases as evinced after their reconstitution into liposomes. Yet phospholipid scrambling is not detectable in the resting plasma membrane of mammalian cells that is replete with GPCRs. We considered whether cholesterol, a prominent component of the plasm...

SARS-CoV-2 is a health threat with dire socioeconomical consequences. As the crucial mediator of infection, the viral glycosylated Spike protein (S) has attracted the most attention and is at the center of efforts to develop therapeutics and diagnostics. Herein, we use an original decomposition approach to identify energetically uncoupled substruct...

Betacoronavirus SARS-CoV-2 is posing a major threat to human health and its diffusion around the world is having dire socioeconomical consequences. Thanks to the scientific community’s unprecedented efforts, the atomic structure of several viral proteins has been promptly resolved. As the crucial mediator of host cell infection, the heavily glycosy...

A fundamental requirement to predict the native conformation, address questions of sequence design and optimization, and gain insights into the folding mechanisms of proteins, lies in the definition of an unbiased reaction coordinate that reports on the folding state without the need to compare it to reference values, which might be unavailable for...

Understanding the selectivity of a small molecule for its target(s) in cells is an important goal in chemical biology and drug discovery. One powerful way to address this question is with dominant negative (DN) mutants, in which an active site residue in the putative target is mutated. While powerful, this approach is less straightforward for allos...

G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Much has been learned about the molecular mechanisms of ligand-GPCR complexes from Molecular Dynamics (...

G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Much has been learned about the molecular mechanisms of ligand-GPCR complexes from Molecular Dynamics (...

This chapter provides a critical overview of the current understanding of allosteric regulation. It provides examples of how this can be integrated with structural knowledge, binding site identification methods, and drug design approaches in the discovery of novel biologically active hits. Allostery constitutes the basis underlying major regulatory...

Allosteric inhibitors can be more difficult to optimize without an understanding of how their binding influences the conformational motions of the target. Here, we used an integrated computational and experimental approach to probe the molecular mechanism of an allosteric inhibitor of heat shock protein 70 (Hsp70). The anticancer compound, MKT-077,...

Here, we introduce a novel computational method to identify the protein substructures most likely to support the functionally-oriented structural deformations that occur upon ligand-binding. To this aim, we study of the modulation of protein energetics along the trajectory of a Molecular Dynamics simulation of different proteins in the presence and...

Molecular chaperones HSP90 and HSP70 are essential regulators of the folding and activation of a disparate ensemble of client proteins. They function through ATP hydrolysis and the assembly of multiprotein complexes with co-chaperones and clients. While their therapeutic relevance is recognized, important details underlying the links between ATP-de...

Background: Communication within a protein complex is mediated by physical interactions made among the protomers. Evidence for both the allosteric regulation present among the protomers of the protein oligomer and of the direct effect of membrane composition on this regulation has made it essential to investigate the underlying molecular mechanism...

Several class-A G protein-coupled receptor (GPCR) proteins act as constitutive phospholipid scramblases catalyzing the transbilayer translocation of >10,000 phospholipids per second when reconstituted into synthetic vesicles. To address the molecular mechanism by which these proteins facilitate rapid lipid scrambling, we carried out large-scale ens...

With the aim of investigating the relationship between the fast fluctuations of proteins and their allosteric behavior, we perform Molecular Dynamics simulations of two model PDZ domains with differential allosteric responses. We focus on protein dynamics in the THz regime (0.1-3 THz) as opposed to lower frequencies. By characterizing the dynamic m...

G protein-coupled receptors (GPCRs) are ubiquitously expressed transmembrane proteins associated with a wide range of diseases such as Alzheimer's, Parkinson, schizophrenia, and also implicated in in several abnormal heart conditions. As such, this family of receptors is regarded as excellent drug targets. However, due to the high number of intrace...

Invited for the cover of this issue is the group of Pierangelo Metrangolo at the Politecnico di Milano. The image depicts the steric zipper formed by the amyloidogenic peptide, DFNKF. Read the full text of the article at 10.1002/chem.201604639.

The amyloidogenic peptide, DFNKF, forms a steric zipper. Iodination of this widely studied sequence facilitated crystallization and allowed its high-resolution single crystal structure determination for the first time. The structure unveils the importance of aromatic–aromatic interactions in stabilizing the amyloid self-assembly. The amino acid sid...

Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report that the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure o...

Heat shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone responsible for the activation, maturation and trafficking of several hundred client proteins in the cell. It is well known that (but not understood how) residues far away from Hsp90’s nucleotide binding pocket can regulate its ATPase activity, a phenomenon called allosteric regu...

Proteins in the arrestin family exhibit a conserved structural fold that nevertheless allows for significant differences in their selectivity for G-protein-coupled-receptors (GPCRs) and their phosphorylation states. To reveal the mechanism of activation that prepares arrestin for selective interaction with GPCRs, and to understand the basis for the...

Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks loca...

The Hsp70 is an allosterically regulated family of molecular chaperones. They consist of two structural domains, NBD and SBD, connected by a flexible linker. ATP hydrolysis at the NBD modulates substrate recognition at the SBD, while peptide binding at the SBD enhances ATP hydrolysis. In this study we apply Molecular Dynamics (MD) to elucidate the...

Allostery is a general phenomenon in proteins whereby a perturbation at one site reverberates into a functional change at another one, through modulation of its conformational dynamics. Herein, we address the problem of how the molecular signal encoded by a ligand is differentially transmitted through the structures of two homologous PDZ proteins:...

Crystallographic structures of NGF/p75NTR and proNGF/p75NTR were previously obtained in 2:1 and 2:2 stoichiometries, respectively. However, evidence shows that both stoichiometries can occur for mature neurotrophins and pro-neurotrophins. We used Molecular Dynamics (MD) simulations to examine the energetic and structural characteristics of these tw...

The recent advances in the in meso crystallization technique for the structural characterization of G-protein coupled receptor (GPCR) proteins have established the usefulness of the lipidic-cubic phases (LCPs) in the field of crystallography of membrane proteins. It is surprising, that despite the success of the approach, the molecular mechanisms o...

Activated Protein C (APC) is a multifunctional serine protease, primarily known for its anticoagulant function in the coagulation system. Several studies have already elucidated its role in counteracting apoptosis and inflammation in cells, while significant effort is still ongoing for defining its involvement in sepsis. Earlier literature has show...

Workflows are very common in bioinformatics because they allow the elaboration of data by delegating the resources management to the information streaming. By the composition of different analysis tools, in fact, it is possible to follow the complex evolution of the biological process. The Web Services technology is very important in this context b...

Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comp...

Author Summary Allostery, or the capability of proteins to respond to ligand binding events with a variation in structure or dynamics at a distant site, is a common feature for biomolecular function and regulation in a large number of proteins. Intra-protein connections and inter-residue coordinations underlie allosteric mechanisms and react to bin...

Map of distance fluctuations of closed DnaK (A), open DnaK (B) and Sse1 (C) complexes. Matrix of distance fluctuations calculated for the three MD trajectories for each ATP, ADP and apo complex. Matrix entries are colored black if below 0.3 and white if above 0.3 Å2, to highlight differences in rigidity pattern among the different complexes. (TIFF)

RMSD of NBD (A, C) and SBD (B, D) of open, closed DnaK and Sse1 Bound to ADP (A, B) or ATP (C, D). RMSD of the single trajectories, calculated fitting the backbone atoms. In red, orange and yellow the closed DnaK trajectories; in blue, light blue and green the open DnaK trajectories; and in violet, magenta and dark violet the Sse1 trajectories. (TI...

RMSD map. Map of time dependent RMSD comparison (snapshot to snapshot RMSD calculated on proteins Cα) between the III MD run starting from ATP-bound closed DnaK complex and the I MD run starting from ADP-bound open DnaK complex, showing an RMSD decrease towards the end of the trajectory, hence a convergent MD evolution to intermediate, semi-open si...

Trajectory clustering results. The number of clusters obtained fitting on Total, NBD or SBD residues is specified in brackets, the percentage represents the number of conformations belonging to the most populated cluster. (DOCX)

Secondary structure comparison. Secondary structure composition of 100 conformations selected from the closed DnaK, open DnaK and Sse1 apo form trajectories. (TIFF)

Map of distance fluctuations of apo complexes. Matrix of distance fluctuations calculated and averaged over the three MD trajectories for each apo complex. Matrix entries are colored black if below 0.3 and white if above 0.3 Å2, to highlight differences in rigidity pattern among the different complexes. Top, closed DnaK; middle, open DnaK; bottom,...

Persistence of the most populated hydrogen bonds during the single trajectories. Percentage of presence, during the single simulation, for each hydrogen bond involved in the identified network. (DOCX)

SBD opening in closed-ATP complex. Representative cluster conformations of closed DnaK SBD bound to ADP (red) and to ATP (green). (TIFF)

Normal mode analysis. ENM-based analysis of homology modeled open DnaK (here referred to as Hsp70) and of open Sse1 (Hsp110). By superimposing extreme structures as obtained by AD-ENM Web server the motion along the first three normal modes (first, blue; second, grey; third, red) is shown (see main text). The sequence stretch 500–527 in Hsp110 was...

Geometric strain analysis of closed DnaK bound to ATP. In the presence of ATP, the closed structure initially shows accumulation of strain at loop 210 in subdomain IIA and segment 152–165 in subdomain IA, which relaxes when lobe I and II become more tightly in contact. The rearrangement of segment 152–165 induces interaction and strain increase at...

Geometric strain analysis of open DnaK bound to ADP. In the open DnaK bound to ADP, a significant strain accumulation indicates approaching between residues of loop 220–224, and the opposite loop area of βSBD, residues 447–452, that progressively rearranges its contact with the NBD. Strain increases at hinges at the C-terminal end, D385, which is p...

Transition pathway connecting the two DnaK open and closed states. Snapshots are extracted from the steepest-descent paths connecting open and closed DnaK structures, as obtained by applying the AD-ENM Web server (see main text). NBD lobe I is colored in green, lobe II is in light blue, βSBD is shown in yellow and αSBD is in red. (TIFF)

Antibody-antigen recognition plays a key role in the immune response against pathogens. Here, we have investigated various aspects of this problem by analyzing a large and diverse set of antibodies and their respective complexes with protein antigens through atomistic simulations. Common features of antibody responses to the presence of antigens ar...

Proteins carry out their functions through interactions with different partners. Dynamic conformational switching among different structural sub-states favors the adaptation to the shapes of the different partners. Such conformational changes can be determined by diverse biochemical factors, such as ligand-binding. Atomic level investigations of th...

The dynamic properties of proteins underlie every aspect of their functions in the cell. The atomistic description of protein motions and their inclusion in ligand selection processes may provide new opportunities for hit identification and drug discovery. Herein, we present a novel rational strategy that allowed us to computationally select new N-...

Local unpacking of aromatic residues observed at the Middle domain in the presence of ADP. A Left, Grp94 starting conformation. Right, end conformation detail of the three helix bundle, with Phe484 and Phe432 shown as VdW spheres, in the ATP and in the ADP simulation respectively. B, same as above, but for Hsp90. Phe364 and Phe421 are shown as VdW...

Representative structures of the most populated clusters of the N-terminal domain in Grp94, highlighting the relative populations and the conformations of the ATP-lid (red tubes). (TIF)

Upper plot: Time evolution of the distance between the centers of mass of the two ADP molecules, bound to the N-terminal domains of Grp94, showing the opening of the dimer clamp during the MD trajectory. Lower plot: Time evolution of the distance between the sidechains of Phe484 and Phe432 of each protomer during the same MD trajectory, showing the...

Time evolution of geometrical strain of a Grp94 (A), Hsp90 (B) and HtpG (C) monomer in the presence of ADP. The units are Å2. (TIF)

Coordinate file for the final structure of the HtpG-ADP simulation. (TXT)

Coordinate file for the final structure of the HtpG-ATP simulation. (TXT)

Coordinate file for the final structure of the Grp94-ATP simulation. (TXT)

Coordinate file for the final structure of the Hsp90-ADP simulation. (TXT)

Coordinate file for the final structure of the Grp94-ADP simulation. (TXT)

Coordinate file for the final structure of the Hsp90-ATP simulation. (TXT)

Solid backbone: HtpG meta-trajectory. The meta-trajectory consists of all protomeric snapshots (restricted to the 525 amino acids alignable with Grp94 and Hsp90) of HtpG in the Apo, ADP- and ATP-bound states. The faint backbone represents the best fit to the Grp94 protomers obtained by suitably rotating the two terminal quasi-rigid domains of proto...

The subdivision of protein structures into smaller and independent structural domains has a fundamental importance in understanding protein evolution and function and in the development of protein classification methods as well as in the interpretation of experimental data. Due to the rapid growth in the number of solved protein structures, the nee...

Author Summary Understanding the connections between structure, binding, dynamics and function in proteins is one of the most fascinating problems in biology and is actively investigated experimentally and computationally. In the latter context, significant advancements are possible by exposing the causal link between the fine atomic-scale protein-...

The interplay of protein dynamics and molecular recognition is of fundamental importance in biological processes. Atomic-resolution insights into these phenomena may provide new opportunities for drug discovery. Herein, we have combined NMR relaxation experiments and residual dipolar coupling (RDC) measurements with molecular dynamics (MD) simulati...

Protein-DNA recognition underlies fundamental biological processes ranging from transcription to replication and modification. Herein, we present a computational study of the sequence modulation of internal dynamic properties and of intraprotein networks of aminoacid interactions that determine the stability and specificity of protein-DNA complexes...

Average pair interaction energies for 1A1F Complex and their standard deviations.

Average pair interaction energies for 1A1G Complex and their standard deviations.

Average pair interaction energies for 1A1I Complex and their standard deviations.

Sequence alignment and structural time evolution of proteins in simulations. Figure S1: The sequence alignment of the protein residues, made with Clustal-W. Figure S2.The time dependent RMSD evolution of all trajectories over the combined molecular dynamic trajectories.

Average pair interaction energies for 1A1J Complex and their standard deviations.

Average pair interaction energies for 1A1L Complex and their standard deviations.

Average pair interaction energies for 1AAY Complex and their standard deviations.

Average pair interaction energies for 1A1K Complex and their standard deviations.