A BIM-enabled Decision Support System to support large-scale energy retrofitting processes and off-site solutions for envelope insulation

The urgency of renewing the Architecture, Engineering and Construction related processes to increase quality standards and performances while reducing costs and operations time is widely discussed in literature. In this scenario, increasing the energy renovation rate of the existing European building stock is a key priority to support the EU's 2050 decarbonisation targets through innovative solutions. The introduction of prefabricated panels for building renovation – incorporating insulation, mechanical systems, and finishing – can provide the existing buildings with improved structural, thermal, acoustic, and architectural features. The higher quality and safety for the off-site activities, the faster on-site application and the reduction of waste are some advantages of this typology of Modern Methods of Construction (MMC). Several digital and informative tools have been introduced over the last years to customize and integrate the design of prefabricated panels on existing building envelopes (i.e. panelisation tools). However, the comparison of technological alternatives is left to the intuition of designers and managed through the use of several tools that are not interconnected and often downstream the design process. This paper presents a Panelisation Design Tool, which is a Decision Support System (DSS) to help decision-makers in the choice of technological solutions for retrofitting operations during the Early Design Stage. Thanks to BIM integration, some indicators related to different aspects (n Dimensions) are extracted from the model of the panelised building to compare different technologies in a systematic way. The Panelisation Design Tool is tested on a case study building located in the city of Monza, in Northern Italy, used as a pilot in the BIM4EEB European Project. The test aimed at demonstrating the effectiveness of the chosen parameters to evaluate multiple technological solutions in an integrated BIM approach

Unexpected dynamics in femtomolar complexes of binding proteins with peptides

Ultra-tight binding is usually observed for proteins associating with rigidified molecules. Previously, we demonstrated that femtomolar binders derived from the Armadillo repeat proteins (ArmRPs) can be designed to interact very tightly with fully flexible peptides. Here we show for ArmRPs with four and seven sequence-identical internal repeats that the peptide-ArmRP complexes display conformational dynamics. These dynamics stem from transient breakages of individual protein-residue contacts that are unrelated to overall unbinding. The labile contacts involve electrostatic interactions. We speculate that these dynamics allow attaining very high binding affinities, since they reduce entropic losses. Importantly, only NMR techniques can pick up these local events by directly detecting conformational exchange processes without complications from changes in solvent entropy. Furthermore, we demonstrate that the interaction surface of the repeat protein regularizes upon peptide binding to become more compatible with the peptide geometry. These results provide novel design principles for ultra-tight binders

Repetitions and Iterations: Novel Approaches to Characterize Protein-Peptide Interactions of Designed Armadillo Repeat Proteins by Solution NMR

About 15-40% of all interactions in the cell are estimated to be peptide-protein interactions and consequently designing a scaffold able to interact with a target peptide through a conserved binding mode has potentially many applications in the field of research, diagnostic and therapeutics. The Armadillo project aims to generate a modular binding technology based on natural Armadillo repeat proteins (nArmRPs). The idea is to build a repetitive protein based on modules able to bind a specific dipeptide each, thus simplifying the problem of generating a binder for every single possible peptide combination to just generate modules binding all the possible combinations of a dipeptide. This thesis was generally devoted to develop and apply new approaches to study designed Armadillo repeat proteins (dArmRPs) in solution by NMR. First, an automated iterative approach to refine structure of dArmRPs based on pseudocontact shifts (PCSs) was developed, thoroughly tested and applied to obtain the first ever dArmRPs solution structures. Next, the obtained structures were characterized with a particular focus on the supercoil, which was the structural aspect most altered in crystal structures while also representing a key design feature, and complemented by detailed investigations of binding dynamics. Finally, the N-terminal cap was redesigned from its yeast 3rd generation sequence to a new artificial 4th generation model to overcome stability issues documented during the previous analysis. In conclusion, this work contributes to the progress of the Armadillo project by supplying structural knowledge and binding dynamics of dArmRPs in their native soluble environment to the already existing X-ray-based information

An automated iterative approach for protein structure refinement using pseudocontact shifts

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing

An automated iterative approach for protein structure refinement using pseudocontact shifts

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing

An automated iterative approach for protein structure refinement using pseudocontact shifts

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.ISSN:0925-2738ISSN:1573-500