Wollacott, Andrew M Xue, Chonghua Qin, Qiuyuan Hua, June Bohnuud, Tanggis Viswanathan, Karthik Kolachalama, Vijaya B
Published in
Protein engineering, design & selection : PEDS
Antibodies often undergo substantial engineering en route to the generation of a therapeutic candidate with good developability properties. Characterization of antibody libraries has shown that retaining native-like sequence improves the overall quality of the library. Motivated by recent advances in deep learning, we developed a bi-directional lon...
David, Benoit Arnaud, Philippe Tellier, Charles Sanejouand, Yves-Henri
Published in
Protein engineering, design & selection : PEDS
Using the information available in the sequences of well-characterized transglycosidases found in plants, mutations were introduced in the glycoside hydrolase of the bacterium Thermus thermophilus, with the aim of turning it into an efficient transglycosidase. All mutants happen to have fair catalytic efficiencies, being at worst 25 times less effi...
Buschhaus, Magdalena J Becker, Stefan Porter, Andrew J Barelle, Caroline J
Published in
Protein engineering, design & selection : PEDS
The adaptive immune system of cartilaginous fish (Elasmobranchii), comprising of classical hetero-tetrameric antibodies, is enhanced through the presence of a naturally occurring homodimeric antibody-like immunoglobulin-the new antigen receptor (IgNAR). The binding site of the IgNAR variable single-domain (VNAR) offers advantages of reduced size (
Christensen, Stefan Jarl Badino, Silke Flindt Cavaleiro, Ana Mafalda Borch, Kim Westh, Peter
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Protein engineering, design & selection : PEDS
The glycoside hydrolase (GH) family 6 is an important group of enzymes that constitute an essential part of industrial enzyme cocktails used to convert lignocellulose into fermentable sugars. In nature, enzymes from this family often have a carbohydrate binding module (CBM) from the CBM family 1. These modules are known to promote adsorption to the...
Poghosyan, Armen H Schafer, Nicholas P Lyngsø, Jeppe Shahinyan, Aram A Pedersen, Jan Skov Otzen, Daniel E
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Protein engineering, design & selection : PEDS
Anionic surfactants denature proteins at low millimolar concentrations, yet little is known about the underlying molecular mechanisms. Here, we undertake 1-μs-long atomistic molecular dynamics simulations of the denaturation of acyl coenzyme A binding protein (ACBP) and compare our results with previously published and new experimental data. Since ...
Fernández-Quintero, Monica L Heiss, Martin C Liedl, Klaus R
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Protein engineering, design & selection : PEDS
Antibody engineering of non-human antibodies has focused on reducing immunogenicity by humanization, being a major limitation in developing monoclonal antibodies. We analyzed four series of antibody binding fragments (Fabs) and a variable fragment (Fv) with structural information in different stages of humanization to investigate the influence of t...
Cohan, Megan C Ruff, Kiersten M Pappu, Rohit V
Published in
Protein engineering, design & selection : PEDS
Intrinsically disordered proteins (IDPs) contribute to a multitude of functions. De novo design of IDPs should open the door to modulating functions and phenotypes controlled by these systems. Recent design efforts have focused on compositional biases and specific sequence patterns as the design features. Analysis of the impact of these designs on ...
Gerlza, Tanja Nagele, Michael Gschwandtner, Martha Winkler, Sophie Kungl, Andreas
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Protein engineering, design & selection : PEDS
The chemokine CXCL10 is released by a plethora of cells, including immune and metastatic cancer cells, following stimulation with interferon-gamma. It acts via its GPC receptor on T-cells attracting them to various target tissues. Glycosaminoglycans (GAGs) are regarded as co-receptors of chemokines, which enable the establishment of a chemotactic g...
Alfaro-Chávez, Ana L Liu, Jian-Wei Stevenson, Bradley J Goldman, Adrian Ollis, David L
Published in
Protein engineering, design & selection : PEDS
In the accompanying paper, we described evolving a lipase to the point where variants were soluble, stable and capable of degrading C8 TAG and C8 esters. These variants were tested for their ability to survive in an environment that might be encountered in a washing machine. Unfortunately, they were inactivated both by treatment with a protease use...
Varela, Angela E England, Kevin A Cavagnero, Silvia
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Protein engineering, design & selection : PEDS
The founding principles of protein folding introduced by Christian Anfinsen, together with the numerous mechanistic investigations that followed, assume that protein folding is a thermodynamically controlled process. On the other hand, this review underscores the fact that thermodynamic control is far from being the norm in protein folding, as long...
