NewProt – a protein engineering portal

Schwarte, Andreas; Genz, Maika; Skalden, Lilly; Nobili, Alberto; Vickers, Clare; Melse, Okke; Kuipers, Remko; Joosten, Han; Štourač, Jan; Bendl, Jaroslav; Black, Jon E; Haase, Peter; Baakman, Coos; Damborský, Jiřı́; Bornscheuer, Uwe T.; Vriend, Gert; Venselaar, Hanka

doi:10.1093/protein/gzx024

Cited by 12 publications

(7 citation statements)

References 42 publications

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“…[97] Catalytic Selectivity by Computational Design (CASCO) based on RosettaDesign and in silico screening constitutes another computational advance,a s proposed by Janssen, Baker and co-workers. [98] Thep rotein engineering portal NewProt, [99] set up by Venselaar and collaboraters,f eatures ac ollection of servers which offer useful computational aids in protein engineering,i ncluding Hotspot Wizard developed by Damborsky. [100] Attempts to engineer enzyme stereoselectivity rationally without generating saturation mutagenesis libaries (or those produced by DNAs huffling or epPCR) is treated separately in Section 4.…”

Section: Further Improvements and Extensions Of The Molecular Biologimentioning

confidence: 99%

The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes

et al. 2020

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Directed evolution of stereo‐, regio‐, and chemoselective enzymes constitutes a unique way to generate biocatalysts for synthetically interesting transformations in organic chemistry and biotechnology. In order for this protein engineering technique to be efficient, fast, and reliable, and also of relevance to synthetic organic chemistry, methodology development was and still is necessary. Following a description of early key contributions, this review focuses on recent developments. It includes optimization of molecular biological methods for gene mutagenesis and the design of efficient strategies for their application, resulting in notable reduction of the screening effort (bottleneck of directed evolution). When aiming for laboratory evolution of selectivity and activity, second‐generation versions of Combinatorial Active‐Site Saturation Test (CAST) and Iterative Saturation Mutagenesis (ISM), both involving saturation mutagenesis (SM) at sites lining the binding pocket, have emerged as preferred approaches, aided by in silico methods such as machine learning. The recently proposed Focused Rational Iterative Site‐specific Mutagenesis (FRISM) constitutes a fusion of rational design and directed evolution. On‐chip solid‐phase chemical gene synthesis for rapid library construction enhances library quality notably by eliminating undesired amino acid bias, the future of directed evolution?

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Section: Further Improvements and Extensions Of The Molecular Biologimentioning

confidence: 99%

The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes

et al. 2020

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“…Particularly, the impact of mutations on the stability of proteins is of specific industrial interest and has been the subject of various studies. These tools have also been made available as web servers [ 19 ]. There are also web servers that integrate multiple tools to provide the user with an option to perform a wider gamut of analysis on the mutants of their interest [ 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

“…These tools have also been made available as web servers [ 19 ]. There are also web servers that integrate multiple tools to provide the user with an option to perform a wider gamut of analysis on the mutants of their interest [ 19 , 20 ]. Although these structure dependent methods are effective in deriving the correlation between the mutation and its effect on the protein activity, they are limited by their requirement of the availability of the protein structure.…”

Section: Introductionmentioning

confidence: 99%

Application of fourier transform and proteochemometrics principles to protein engineering

Cadet¹,

Fontaine²,

Vetrivel³

et al. 2018

BMC Bioinformatics

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BackgroundConnecting the dots between the protein sequence and its function is of fundamental interest for protein engineers. In-silico methods are useful in this quest especially when structural information is not available. In this study we propose a mutant library screening tool called iSAR (innovative Sequence Activity Relationship) that relies on the physicochemical properties of the amino acids, digital signal processing and partial least squares regression to uncover these sequence-function correlations.ResultsWe show that the digitalized representation of the protein sequence in the form of a Fourier spectrum can be used as an efficient descriptor to model the sequence-activity relationship of proteins. The iSAR methodology that we have developed identifies high fitness mutants from mutant libraries relying on physicochemical properties of the amino acids, digital signal processing and regression techniques. iSAR correlates variations caused by mutations in spectra with biological activity/fitness. It takes into account the impact of mutations on the whole spectrum and does not focus on local fitness alone. The utility of the method is illustrated on 4 datasets: cytochrome P450 for thermostability, TNF-alpha for binding affinity, GLP-2 for potency and enterotoxins for thermostability. The choice of the datasets has been made such as to illustrate the ability of the method to perform when limited training data is available and also when novel mutations appear in the test set, that have not been featured in the training set.ConclusionThe combination of Fast Fourier Transform and Partial Least Squares regression is efficient in capturing the effects of mutations on the function of the protein. iSAR is a fast algorithm which can be implemented with limited computational resources and can make effective predictions even if the training set is limited in size.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2407-8) contains supplementary material, which is available to authorized users.

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“…Eine fortgeschrittene Methode ist das auf Rosetta und In‐silico‐Screening basierende CASCO (Catalytic Selectivity by Computational Design), entworfen von Janssen, Baker und Mitarbeitern . Das Protein‐Engineering‐Portal NewProt, eingerichtet von Venselaar et al., besteht aus einer Gruppe von Servern, die nützliche Hilfen für das Protein‐Engineering anbieten, einschließlich Hotspot Wizard (Damborsky) . Versuche, Enzym‐Stereoselektivität auf rationaler Basis, d. h. ohne die Erzeugung von SM‐Bibliotheken (oder durch DNA‐Shuffling oder epPCR erzeugte Bibliotheken) zu generieren, werden in Abschnitt 4 separat diskutiert.…”

Section: Strategien Und Techniken Der Sättigungsmutagenese (Sm) Zur Eunclassified

Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme

Acevedo‐Rocha

et al. 2020

Angewandte Chemie

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Die gerichtete Evolution von stereo‐, regio‐ und chemoselektiven Enzymen ist ein einzigartiges Verfahren zur Herstellung von Biokatalysatoren für synthetisch interessante Transformationen. Methodenentwicklung war und bleibt unerlässlich, um diese Technik des Protein‐Engineerings effizient, schnell, zuverlässig und als relevant für die organische Chemie zu gestalten. Dieser Aufsatz widmet sich den jüngsten Entwicklungen auf diesem Gebiet, wobei frühe wichtige Beiträge ebenfalls Beachtung finden. Er schreibt die Optimierung molekularbiologischer Methoden zur Genmutagenese und Strategien für deren effizienten Einsatz, um so den Screeningaufwand (der Engpass in der gerichteten Evolution) möglichst gering zu halten. Im Hinblick auf die laborbasierte Evolution von Selektivität und Aktivität hat sich ergeben, dass fortgeschrittene Versionen von CAST (Combinatorial Active‐site Saturation Test) und iterativer Sättigungsmutagenese (ISM) als spezielle Formen der Sättigungsmutagenese (SM) an der Bindungstasche bevorzugt verwendet werden, unterstützt durch In‐silico‐Methoden wie Maschinellem Lernen. Die jüngst vorgeschlagene FRISM‐Technik (Focused Rational Iterative Site‐specific Mutagenesis) gilt als Fusion von rationalem Design und gerichteter Evolution. Die chemische Festphasensynthese von Genen auf einem Chip zum schnellen Bibliotheksaufbau vermeidet eine unerwünschte Präferenz spezifischer Aminosäuren und verbessert die Qualität von Substanzbibliotheken erheblich – ist dies die Zukunft der gerichteten Evolution?

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NewProt – a protein engineering portal

Cited by 12 publications

References 42 publications

The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes

The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes

Application of fourier transform and proteochemometrics principles to protein engineering

Die zentrale Rolle der Methodenentwicklung in der gerichteten Evolution selektiver Enzyme

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