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2. In vitro selection of DNA aptamers for proteins immobilized on magnetic beads and monitoring of ssDNA pool evolutionNina Mencin, 2015, doctoral dissertation Found in: ključnih besedah
Summary of found: ...aptamer, SELEX, protocol optimization, pool evolution monitoring, protein Cdc45...
Keywords: aptamer, SELEX, protocol optimization, pool evolution monitoring, protein Cdc45
Published: 01.04.2015; Views: 4790; Downloads: 292
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3. In vitro selection of DNA aptamers for proteins immobilized on magnetic beads and monitoring of ssDNA pool evolutionNina Mencin, 2015, doctoral dissertation Found in: ključnih besedah
Summary of found: ...aptameri, SELEX, optimizacija protokola, protein Cdc45, disertacije, ...
Keywords: aptameri, SELEX, optimizacija protokola, protein Cdc45, disertacije
Published: 10.07.2015; Views: 3900; Downloads: 141
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4. Computational design of customised nanobodies for biotechnological applicationsSara Fortuna, Ario de Marco, Miguel Soler, 2016, unpublished conference contribution Abstract: In silico modeling to improve the biophysical characteristics of recombinant single-domain antibodies
Found in: ključnih besedah
Summary of found: ...nanobodies, modeling, protein stability, antibody humanization, molecular dynamics...
Keywords: nanobodies, modeling, protein stability, antibody humanization, molecular dynamics
Published: 26.04.2016; Views: 3498; Downloads: 0
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5. Entropic cost of folding and phase diagrams of polypeptides: Why are IDPs unfolded at room temperature?Artem Badasyan, invited lecture at foreign university Abstract: In spin models, that are applied to describe the conformational transitions in polymers, the number of spin orientations, that correspond to the disordered conformation, can be estimated using fundamental definitions of Statistical Physics. For instance, when considering alpha-helix to coil transition in polypeptides, the role of generalized coordinates is played by pairs of torsional angle, and the repeating unit populates different regions of that 2D contour map, depending on conformation. By scanning over all possible torsional angles, that do not violate the obvious limitations due to the excluded volume, the so-called Ramachandran map can be plotted, which is actually the phase space visualization for the helix-coil transition problem. The region of phase space, corresponding to the ordered, helical conformations, is much more limited, than the one, corresponding to all other (allowed) conformations. We can calculate the areas of these regions as Γhelix and Γcoil , and construct the ratio Q = Γcoil . Naturally, it can be interpreted as log(Q) = Scoil − Shelix = ΔS, the entropic cost of helix with respect to coil. To illustrate the importance of the entropic price of ordered conformation we report our recent results, that allowed to explain the peculiarity of phase diagrams of Intrinsically Disordered Proteins (IDP) out of larger Q-values, as compared to globular counterparts. In particular, it has been shown, that due to larger Q, the phase diagram of IDP is shifted towards higher temperatures.
Found in: ključnih besedah
Summary of found: ...IDP, protein folding, phase diagram...
Keywords: IDP, protein folding, phase diagram
Published: 23.06.2016; Views: 3486; Downloads: 0
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6. Human papillomavirus infection requires the TSG101 component of the ESCRT machineryMartina Bergant Marušič, Justyna Broniarczyk, Anna Gozdzicka-Jozefiak, Lawrence Banks, 2014, original scientific article Found in: ključnih besedah
Summary of found: ...humani virusi papiloma, infekcije, protein L2, TSG101, ...
Keywords: humani virusi papiloma, infekcije, protein L2, TSG101
Published: 16.06.2016; Views: 3743; Downloads: 12
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7. An intrabody specific for the nucleophosmin carboxy-terminal mutant and fused to a nuclear localization sequence binds its antigen but fails to relocate it in the nucleusArio De Marco, Chiara Martinelli, Emanuela Colombo, Daniele Piccini, Cristina Sironi, Pier Giuseppe Pelicci, 2014, original scientific article Found in: ključnih besedah
Summary of found: ...intrabody, leukemia, protein shuttling, recombinant fusion protein, single-chain antibody, ...
Keywords: intrabody, leukemia, protein shuttling, recombinant fusion protein, single-chain antibody
Published: 16.06.2016; Views: 3063; Downloads: 17
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8. Recent contributions in the field of the recombinant expression of disulfide bonded proteins in bacteriaArio De Marco, 2012, short scientific article Found in: ključnih besedah
Summary of found: ...recombinant protein expression, disulfide, bonds, redox conditions, ...
Keywords: recombinant protein expression, disulfide, bonds, redox conditions
Published: 16.06.2016; Views: 3020; Downloads: 118
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10. Distance-based configurational entropy of proteins from molecular dynamics simulationsFederico Fogolari, Alessandra Corazza, Sara Fortuna, Miguel Angel Soler, Bryan VanSchouwen, Giorgia Brancolini, Stefano Corni, Giuseppe Melacini, Gennaro Esposito, 2015, original scientific article Abstract: 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.
Found in: ključnih besedah
Summary of found: ...reference entropies for amino acids in unfolded proteins are obtained from a database of residues...
Keywords: entropy, protein, molecular dynamics, simulations, MD
Published: 12.10.2016; Views: 3165; Downloads: 192
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