scholarly journals Computational Design of a Biologically Active Enzyme

Science ◽  
2004 ◽  
Vol 304 (5679) ◽  
pp. 1967-1971 ◽  
Author(s):  
M. A. Dwyer
2019 ◽  
Vol 60 (1) ◽  
pp. 332-341 ◽  
Author(s):  
Maninder Singh ◽  
Vikash Kumar ◽  
Kamakshi Sikka ◽  
Ravi Thakur ◽  
Munesh Kumar Harioudh ◽  
...  

1989 ◽  
Vol 161 (2) ◽  
pp. 865-872 ◽  
Author(s):  
E. Ciccarelli ◽  
M. Massaer ◽  
J.-P. Guillaume ◽  
A. Herzog ◽  
R. Loriau ◽  
...  

2020 ◽  
Author(s):  
Ariel J. Ben-Sasson ◽  
Joseph Watson ◽  
William Sheffler ◽  
Matthew Camp Johnson ◽  
Alice Bittleston ◽  
...  

AbstractProteins that assemble into ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers,6,7 but with the exception of a single lattice formed through non-rigid template streptavidin linkers,8 they are constituted from just one protein component. For modulating assembly dynamics and incorporating more complex functionality, materials composed of two components would have considerable advantages.9–12 Here we describe a computational method to generate de-novo binary 2D non-covalent co-assemblies by designing rigid asymmetric interfaces between two distinct protein dihedral building-blocks. The designed array components are soluble at mM concentrations, but when combined at nM concentrations, rapidly assemble into nearly-crystalline micrometer-scale p6m arrays nearly identical to the computational design model in vitro and in cells without the need of a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized, and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces to drive extensive receptor clustering, downstream protein recruitment, and signaling. Using quantitative microscopy we show that arrays assembled on living cells have component stoichiometry and likely structure similar to arrays formed in vitro, suggesting that our material can impose order onto fundamentally disordered substrates like cell membranes. We find further that in sharp contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work paves the way towards synthetic cell biology, where a new generation of multi-protein macroscale materials is designed to modulate cell responses and reshape synthetic and living systems.One Sentence SummaryCo-assembling binary 2D protein crystals enables robust formation of complex large scale ordered biologically active materials


2020 ◽  
Author(s):  
Letícia Cristina Assis ◽  
Alexandre Alves de Castro ◽  
João Paulo Almirão de Jesus ◽  
Eugenie Nepovimova ◽  
Kamil Kuca ◽  
...  

Abstract A new and more aggressive strain of coronavirus, known as SARS-CoV-2, which is highly contagious, has rapidly spread across the planet within a short period of time. Due to its high transmission rate and the significant time–space between infection and manifestation of symptoms, the WHO recently declared this a pandemic. Because of the exponentially growing number of new cases of both infections and deaths, development of new therapeutic options to help fight this pandemic is urgently needed. The target molecules of this study were the nitro derivatives of quinoline and quinoline N-oxide. Computational design at the DFT level, docking studies, and molecular dynamics methods as a well-reasoned strategy will aid in elucidating the fundamental physicochemical properties and molecular functions of a diversity of compounds, directly accelerating the process of discovering new drugs. In this study, we discovered isomers based on the nitro derivatives of quinoline and quinoline N-oxide, which are biologically active compounds and may be low-cost alternatives for the treatment of infections induced by SARS-CoV-2.


2010 ◽  
Vol 518 (19) ◽  
pp. 5615-5621 ◽  
Author(s):  
Lise T. de Jonge ◽  
J. Ju ◽  
S.C.G. Leeuwenburgh ◽  
Y. Yamagata ◽  
T. Higuchi ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Letícia C. Assis ◽  
Alexandre A. de Castro ◽  
João P. A. de Jesus ◽  
Eugenie Nepovimova ◽  
Kamil Kuca ◽  
...  

AbstractA new and more aggressive strain of coronavirus, known as SARS-CoV-2, which is highly contagious, has rapidly spread across the planet within a short period of time. Due to its high transmission rate and the significant time–space between infection and manifestation of symptoms, the WHO recently declared this a pandemic. Because of the exponentially growing number of new cases of both infections and deaths, development of new therapeutic options to help fight this pandemic is urgently needed. The target molecules of this study were the nitro derivatives of quinoline and quinoline N-oxide. Computational design at the DFT level, docking studies, and molecular dynamics methods as a well-reasoned strategy will aid in elucidating the fundamental physicochemical properties and molecular functions of a diversity of compounds, directly accelerating the process of discovering new drugs. In this study, we discovered isomers based on the nitro derivatives of quinoline and quinoline N-oxide, which are biologically active compounds and may be low-cost alternatives for the treatment of infections induced by SARS-CoV-2.


Author(s):  
Kathleen M. Marr ◽  
Mary K. Lyon

Photosystem II (PSII) is different from all other reaction centers in that it splits water to evolve oxygen and hydrogen ions. This unique ability to evolve oxygen is partly due to three oxygen evolving polypeptides (OEPs) associated with the PSII complex. Freeze etching on grana derived insideout membranes revealed that the OEPs contribute to the observed tetrameric nature of the PSIl particle; when the OEPs are removed, a distinct dimer emerges. Thus, the surface of the PSII complex changes dramatically upon removal of these polypeptides. The atomic force microscope (AFM) is ideal for examining surface topography. The instrument provides a topographical view of individual PSII complexes, giving relatively high resolution three-dimensional information without image averaging techniques. In addition, the use of a fluid cell allows a biologically active sample to be maintained under fully hydrated and physiologically buffered conditions. The OEPs associated with PSII may be sequentially removed, thereby changing the surface of the complex by one polypeptide at a time.


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