scholarly journals Author response: Precise assembly of complex beta sheet topologies from de novo designed building blocks

2015 ◽  
Author(s):  
Indigo Chris King ◽  
James Gleixner ◽  
Lindsey Doyle ◽  
Alexandre Kuzin ◽  
John F Hunt ◽  
...  
Keyword(s):  
De Novo ◽  
Building Blocks ◽  
Author Response ◽  
Beta Sheet

scholarly journals Precise assembly of complex beta sheet topologies from de novo designed building blocks

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Indigo Chris King ◽  
James Gleixner ◽  
Lindsey Doyle ◽  
Alexandre Kuzin ◽  
John F Hunt ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Design ◽  
Building Blocks ◽  
Beta Sheets ◽  
Protein Domain ◽  
Beta Sheet ◽  
Design Models ◽  
Natural Protein ◽  
Complex Protein ◽  
Alpha Beta

Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution.

De Novo Synthesis of l-Colitose and l-Rhodinose Building Blocks

2011 ◽  
Vol 77 (2) ◽  
pp. 870-877 ◽  
Author(s):  
Oliviana Calin ◽  
Rajan Pragani ◽  
Peter H. Seeberger
Keyword(s):  
De Novo ◽  
Building Blocks ◽  
De Novo Synthesis

Author response for "Novel and de novo point and large microdeletion mutation in PRRT2 -related epilepsy"

2020 ◽  
Author(s):  
Li Yang ◽  
Cuiping You ◽  
Shiyan Qiu ◽  
Xiaofan Yang ◽  
Yufen Li ◽  
...  
Keyword(s):  
De Novo ◽  
Author Response

scholarly journals De novo design of self-assembling helical protein filaments

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. 705-709 ◽  
Author(s):  
Hao Shen ◽  
Jorge A. Fallas ◽  
Eric Lynch ◽  
William Sheffler ◽  
Bradley Parry ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Design ◽  
Building Blocks ◽  
Repeat Units ◽  
Self Assembling ◽  
Wide Range ◽  
Helical Protein ◽  
Monomeric Proteins

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

scholarly journals Author response: A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation

2017 ◽  
Author(s):  
Meng Amy Li ◽  
Paulo P Amaral ◽  
Priscilla Cheung ◽  
Jan H Bergmann ◽  
Masaki Kinoshita ◽  
...  
Keyword(s):  
Dna Methylation ◽  
State Transition ◽  
De Novo ◽  
Author Response ◽  
Cell State ◽  
A Cell

scholarly journals ROBUSTNESS-STRENGTH PERFORMANCE OF HIERARCHICAL ALPHA-HELICAL PROTEIN FILAMENTS

2009 ◽  
Vol 01 (01) ◽  
pp. 85-112 ◽  
Author(s):  
ZHAO QIN ◽  
STEVEN CRANFORD ◽  
THEODOR ACKBAROW ◽  
MARKUS J BUEHLER
Keyword(s):  
De Novo ◽  
Hierarchical Structures ◽  
High Strength ◽  
Material Design ◽  
Building Blocks ◽  
Biological Materials ◽  
Strength Performance ◽  
Synthetic Materials ◽  
Helical Protein ◽  
Bioinspired Nanomaterials

An abundant trait of biological protein materials are hierarchical nanostructures, ranging through atomistic, molecular to macroscopic scales. By utilizing the recently developed Hierarchical Bell Model, here we show that the use of hierarchical structures leads to an extended physical dimension in the material design space that resolves the conflict between disparate material properties such as strength and robustness, a limitation faced by many synthetic materials. We report materiomics studies in which we combine a large number of alpha-helical elements in all possible hierarchical combinations and measure their performance in the strength-robustness space while keeping the total material use constant. We find that for a large number of constitutive elements, most random structural combinations of elements (> 98%) lead to either high strength or high robustness, reflecting the so-called banana-curve performance in which strength and robustness are mutually exclusive properties. This banana-curve type behavior is common to most engineered materials. In contrast, for few, very specific types of combinations of the elements in hierarchies (< 2%) it is possible to maintain high strength at high robustness levels. This behavior is reminiscent of naturally observed material performance in biological materials, suggesting that the existence of particular hierarchical structures facilitates a fundamental change of the material performance. The results suggest that biological materials may have developed under evolutionary pressure to yield materials with multiple objectives, such as high strength and high robustness, a trait that can be achieved by utilization of hierarchical structures. Our results indicate that both the formation of hierarchies and the assembly of specific hierarchical structures play a crucial role in achieving these mechanical traits. Our findings may enable the development of self-assembled de novo bioinspired nanomaterials based on peptide and protein building blocks.

A de novo Synthesis of Oxindoles from Cyclohexanone-Derived γ-Keto-ester Acceptors Using a Desaturative Amination–Cyclization Approach

Synthesis ◽  
2021 ◽  
Author(s):  
Henry P. Caldora ◽  
Sebastian Govaerts ◽  
Shashikant U. Dighe ◽  
Oliver J. Turner ◽  
Daniele Leonori
Keyword(s):  
Amino Acids ◽  
Primary Amine ◽  
De Novo ◽  
Building Blocks ◽  
De Novo Synthesis ◽  
Keto Ester ◽  
Mild Conditions ◽  
Blockbuster Drug

Here we report a desaturative approach for oxindole synthesis. This method uses simple γ-ester-containing cyclohexanones and primary amine building blocks as coupling partners. A dual photoredox–cobalt manifold is used to generate a secondary aniline that, upon heating, cyclizes with the pendent ester functionality. The process operates under mild conditions and was applied to the modification of several amino acids, the blockbuster drug mexiletine, as well as the formation of dihydroquinolinones.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

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