scholarly journals Intein-assisted bisection mapping systematically splits proteins for Boolean logic and inducibility engineering

2020 ◽  
Author(s):  
Trevor Y. H. Ho ◽  
Alexander Shao ◽  
Zeyu Lu ◽  
Harri Savilahti ◽  
Filippo Menolascina ◽  
...  
Keyword(s):  
Protein Function ◽  
Logic Gates ◽  
Identification Problem ◽  
Boolean Logic ◽  
Host Protein ◽  
Structure Alignment ◽  
Protein Activity ◽  
Homologous Proteins ◽  
Split Protein ◽  
Rational Inference

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.

scholarly journals A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trevor Y. H. Ho ◽  
Alexander Shao ◽  
Zeyu Lu ◽  
Harri Savilahti ◽  
Filippo Menolascina ◽  
...  
Keyword(s):  
Logic Gate ◽  
Logic Gates ◽  
Identification Problem ◽  
Boolean Logic ◽  
Structure Alignment ◽  
Homologous Proteins ◽  
Highly Active ◽  
Split Protein ◽  
Rational Inference ◽  
Site Identification

AbstractSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.

scholarly journals Digital logic gates in soft, conductive mechanical metamaterials

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Charles El Helou ◽  
Philip R. Buskohl ◽  
Christopher E. Tabor ◽  
Ryan L. Harne
Keyword(s):  
Integrated Circuits ◽  
Electronic Materials ◽  
Polymer Networks ◽  
Conductive Polymer ◽  
Network Connectivity ◽  
Logic Gates ◽  
Boolean Logic ◽  
Digital Logic ◽  
Mechanical Metamaterials ◽  
Logic Operations

AbstractIntegrated circuits utilize networked logic gates to compute Boolean logic operations that are the foundation of modern computation and electronics. With the emergence of flexible electronic materials and devices, an opportunity exists to formulate digital logic from compliant, conductive materials. Here, we introduce a general method of leveraging cellular, mechanical metamaterials composed of conductive polymers to realize all digital logic gates and gate assemblies. We establish a method for applying conductive polymer networks to metamaterial constituents and correlate mechanical buckling modes with network connectivity. With this foundation, each of the conventional logic gates is realized in an equivalent mechanical metamaterial, leading to soft, conductive matter that thinks about applied mechanical stress. These findings may advance the growing fields of soft robotics and smart mechanical matter, and may be leveraged across length scales and physics.

Optobiochemistry: Genetically Encoded Control of Protein Activity by Light

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Jihye Seong ◽  
Michael Z. Lin
Keyword(s):  
Protein Function ◽  
Living Cells ◽  
Optical Methods ◽  
Annual Review ◽  
Publication Date ◽  
Protein Activity ◽  
Spatiotemporal Resolution ◽  
Protein Functions ◽  
Protein Classes ◽  
Control Protein

Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light.Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Targeting Acute Myeloid Leukemia Using the RevCAR Platform: A Programmable, Switchable and Combinatorial Strategy

Cancers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 4785
Author(s):  
Enrico Kittel-Boselli ◽  
Karla Elizabeth González Soto ◽  
Liliana Rodrigues Loureiro ◽  
Anja Hoffmann ◽  
Ralf Bergmann ◽  
...  
Keyword(s):  
T Cells ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Immune Escape ◽  
Early Stage ◽  
Logic Gates ◽  
Boolean Logic ◽  
In Vivo Models ◽  
Peptide Epitope ◽  
Acute Myeloid

Clinical translation of novel immunotherapeutic strategies such as chimeric antigen receptor (CAR) T-cells in acute myeloid leukemia (AML) is still at an early stage. Major challenges include immune escape and disease relapse demanding for further improvements in CAR design. To overcome such hurdles, we have invented the switchable, flexible and programmable adaptor Reverse (Rev) CAR platform. This consists of T-cells engineered with RevCARs that are primarily inactive as they express an extracellular short peptide epitope incapable of recognizing surface antigens. RevCAR T-cells can be redirected to tumor antigens and controlled by bispecific antibodies cross-linking RevCAR T- and tumor cells resulting in tumor lysis. Remarkably, the RevCAR platform enables combinatorial tumor targeting following Boolean logic gates. We herein show for the first time the applicability of the RevCAR platform to target myeloid malignancies like AML. Applying in vitro and in vivo models, we have proven that AML cell lines as well as patient-derived AML blasts were efficiently killed by redirected RevCAR T-cells targeting CD33 and CD123 in a flexible manner. Furthermore, by targeting both antigens, a Boolean AND gate logic targeting could be achieved using the RevCAR platform. These accomplishments pave the way towards an improved and personalized immunotherapy for AML patients.

Boolean Logic

2021 ◽  
Vol 48 (2) ◽  
pp. 177-191
Author(s):  
Martin Frické
Keyword(s):  
Probability Theory ◽  
Boolean Algebra ◽  
Programming Languages ◽  
Propositional Logic ◽  
Logic Gates ◽  
Boolean Logic ◽  
Database Queries ◽  
Electrical Switching ◽  
Set Operations ◽  
Set Membership

The article describes and explains Boolean logic (or Boolean algebra) in its two principal forms: that of truth-values and the Boolean connectives and, or, and not, and that of set membership and the set operations of intersection, union and complement. The main application areas of Boolean logic to know­ledge organization, namely post-coordinate indexing and search, are introduced and discussed. Some wider application areas are briefly mentioned, such as: propositional logic, the Shannon-style approach to electrical switching and logic gates, computer programming languages, probability theory, and database queries. An analysis is offered of shortcomings that Boolean logic has in terms of potential uses in know­ledge organization.

scholarly journals TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses

2020 ◽  
Vol 48 (W1) ◽  
pp. W72-W76 ◽  
Author(s):  
Vadim M Gumerov ◽  
Igor B Zhulin
Keyword(s):  
Protein Function ◽  
Computational Study ◽  
Function Analysis ◽  
Domain Architecture ◽  
Protein Domain ◽  
Homologous Proteins ◽  
Gene Neighborhood ◽  
Protein Domain Architecture ◽  
Key Steps

Abstract Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. TREND is freely available at http://trend.zhulinlab.org.

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