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1.
Computational design of customised nanobodies for biotechnological applications
Sara Fortuna, Ario de Marco, Miguel Soler, 2016, prispevek na konferenci brez natisa

Opis: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Najdeno v: ključnih besedah
Povzetek najdenega: ...nanobodies, modeling, protein stability, antibody humanization, molecular dynamics...
Ključne besede: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Objavljeno: 26.04.2016; Ogledov: 1377; Prenosov: 0
.pdf Polno besedilo (2,42 MB)

2.
Distance-based configurational entropy of proteins from molecular dynamics simulations
Federico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, izvirni znanstveni članek

Opis: Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements; the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state; backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy); the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.
Najdeno v: ključnih besedah
Ključne besede: entropy, protein, molecular dynamics, simulations, MD
Objavljeno: 12.10.2016; Ogledov: 1225; Prenosov: 118
.pdf Polno besedilo (2,40 MB)

3.
Accurate estimation of the entropy of rotation-translation probability distributions
Federico Fogolari, Cedrix Jurgal Dongmo Foumthuim, Sara Fortuna, Miguel Angel Soler, Alessandra Corazza, Gennaro Esposito, 2016, izvirni znanstveni članek

Opis: The estimation of rotational and translational entropies in the context of ligand binding has been the subject of long-time investigations. The high dimensionality (six) of the problem and the limited amount of sampling often prevent the required resolution to provide accurate estimates by the histogram method. Recently, the nearest-neighbor distance method has been applied to the problem, but the solutions provided either address rotation and translation separately, therefore lacking correlations, or use a heuristic approach. Here we address rotational–translational entropy estimation in the context of nearest-neighbor-based entropy estimation, solve the problem numerically, and provide an exact and an approximate method to estimate the full rotational–translational entropy.
Najdeno v: ključnih besedah
Povzetek najdenega: ...entropy, probability distribution, molecular dynamics, nearest-neighbor...
Ključne besede: entropy, probability distribution, molecular dynamics, nearest-neighbor
Objavljeno: 11.10.2016; Ogledov: 1290; Prenosov: 0
.pdf Polno besedilo (1,47 MB)

4.
Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Ario de Marco, Miguel Soler, Sara Fortuna, 2016, izvirni znanstveni članek

Opis: Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Najdeno v: ključnih besedah
Ključne besede: nanobodies, molecular dynamics, modeling, antibody solubility
Objavljeno: 11.10.2016; Ogledov: 1451; Prenosov: 134
.pdf Polno besedilo (1,95 MB)

5.
Nanobodies: towards rational design of immune-reagents
Ario De Marco, 2017, objavljeni povzetek znanstvenega prispevka na konferenci (vabljeno predavanje)

Opis: Antibodies are irreplaceable reagents in both research and clinical practice. Despite their relevance, the structural complexity of conventional mono- and polyclonal antibodies (IgG) has always been a limit for their engineering towards reagents optimized for specific applications, such as in vivo diagnostics and therapy. Furthermore, their isolation is time consuming, their production expensive, and their functionalization results often in heterogeneous macromolecule populations. These drawbacks promoted the search for both innovative antibody isolation strategies and alternative scaffolds. In vitro panning of pre-immune collections of recombinant antibody fragments allows for the simple and fast recovery of binders. Since they did not undergo somatic maturation, their affinity for targets can be insufficient but on the other hand they can be rapidly mutated by standard molecular biology techniques to generate second-generation antibodies among which to identify clones with improved characteristics. Both stochastic and rational methods have been proposed for the optimization process. Random mutagenesis followed by panning at stringent conditions has been successful used to select binders with improved physical characteristics. Rational methods try to identify in silico key residues involved in the regulation of specific antibody features, such as stability or binding affinity. The accuracy of these methods usually depends on the calculation resources. In this perspective, smaller molecules can be analyzed “better” than larger because of their restricted number of residues. Nanobodies small dimensions have been long appreciated since enable better tissue penetration, shorter clearance time, higher yields. Now it becomes evident that this characteristic makes them also optimal objects for modeling.
Najdeno v: ključnih besedah
Povzetek najdenega: ...they can be rapidly mutated by standard molecular biology techniques to generate second-generation antibodies among... ...recombinant antibody modeling, nanobody engineering, molecular dynamics and docking...
Ključne besede: recombinant antibody modeling, nanobody engineering, molecular dynamics and docking
Objavljeno: 21.03.2018; Ogledov: 1151; Prenosov: 0
.pdf Polno besedilo (638,20 KB)

6.
The dissociation constant of water at extreme conditions: a molecular dynamics study
Rabi Khanal, 2012, diplomsko delo

Najdeno v: ključnih besedah
Ključne besede: water, molecular dynamics, pK, dissociation, Bluemoon approach
Objavljeno: 21.03.2019; Ogledov: 349; Prenosov: 0
.pdf Polno besedilo (968,81 KB)

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