Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study

2004 ◽  
Vol 58 (3) ◽  
pp. 560-570 ◽  
Author(s):  
John L. Klepeis ◽  
Yinan Wei ◽  
Michael H. Hecht ◽  
Christodoulos A. Floudas
Keyword(s):  
Ab Initio ◽  
De Novo ◽  
Protein A ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Double Blind ◽  
Three Dimensional Structure ◽  
Ab Initio Prediction

scholarly journals Generative Models for Relief Perspective Architectures

2021 ◽  
Author(s):  
Leonardo Baglioni ◽  
Federico Fallavollita
Keyword(s):  
Research Methodology ◽  
Affine Space ◽  
Three Dimensional ◽  
Generative Models ◽  
Linear Perspective ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Present Essay ◽  
Santa Maria

AbstractThe present essay investigates the potential of generative representation applied to the study of relief perspective architectures realized in Italy between the sixteenth and seventeenth centuries. In arts, and architecture in particular, relief perspective is a three-dimensional structure able to create the illusion of great depths in small spaces. A method of investigation applied to the case study of the Avila Chapel in Santa Maria in Trastevere in Rome (Antonio Gherardi 1678) is proposed. The research methodology can be extended to other cases and is based on the use of a Relief Perspective Camera, which can create both a linear perspective and a relief perspective. Experimenting mechanically and automatically the perspective transformations from the affine space to the illusory space and vice versa has allowed us to see the case study in a different light.

De novo design, synthesis and study of albebetin, a polypeptide with a predetermined three-dimensional structure

1992 ◽  
Vol 225 (4) ◽  
pp. 927-931 ◽  
Author(s):  
A.N. Fedorov ◽  
D.A. Dolgikh ◽  
V.V. Chemeris ◽  
B.K. Chernov ◽  
A.V. Finkelstein ◽  
...  
Keyword(s):  
De Novo ◽  
Three Dimensional ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Design Synthesis ◽  
Three Dimensional Structure

scholarly journals Nuclear Magnetic Resonance seq (NMRseq): A New Approach to Peptide Sequence Tags

Toxins ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 437 ◽  
Author(s):  
David Wilson ◽  
Norelle L. Daly
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
De Novo ◽  
Three Dimensional ◽  
Peptide Sequence ◽  
Dimensional Structure ◽  
Amino Acid Type ◽  
Three Dimensional Structure ◽  
Nuclear Magnetic

Structural analysis of peptides with nuclear magnetic resonance (NMR) spectroscopy generally relies on knowledge of the primary sequence to enable assignment of the resonances prior to determination of the three-dimensional structure. Resonance assignment without knowledge of the sequence is complicated by redundancy in amino acid type, making complete de novo sequencing using NMR spectroscopy unlikely to be feasible. Despite this redundancy, we show here that NMR spectroscopy can be used to identify short sequence tags that can be used to elucidate full-length peptide sequences via database searching. In the current study, we have used this approach to identify conotoxins from the venom of the cone snail Conus geographus and determined the three-dimensional structure of a member of the I3 superfamily. This approach is most likely to be useful for the characterization of disulfide-rich peptides, such as those that were chosen for this study, as they generally have well-defined structures, which enhances the quality of the NMR spectra. In contrast to other sequencing methods, the lack of sample manipulation, such as protease digestion, allows for subsequent bioassays to be carried out using the native sample used for sequence identification.

scholarly journals Comparing the fluctuations of the intrinsically disordered C-terminal domain of human SELK free in water and in lipid membrane

2015 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Endoplasmic Reticulum ◽  
Ab Initio ◽  
Lipid Bilayer ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Protein Interaction Data ◽  
Endoplasmic Reticulum Membrane ◽  
Three Dimensional Structure ◽  
Intrinsically Disordered ◽  
Terminal Domain

SELK is a single-pass trans-membrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is resulted to be up-expressed in hepatocellular carcinoma and in other cancers, therefore there is a need to analyze its structure-function relationships. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK, modeled its three-dimensional structure and analyzed its conformational changes by Molecular Dynamics simulations. Our analysis showed that the C-terminal domain of SELK is a weak polyelectrolyte and specifically, a polycation, which has the characteristic molecular signature of natively disordered segments. Since the search by BLAST has not evidenced possible templates with an acceptable sequence identity percentage with the C-terminal sequence of SELK, its three-dimensional structure was modeled by ab initio modeling. The best model is characterized by one short helix and the most part of residues with no regular secondary structure elements. This model was subjected to MD simulation at neutral pH in water to assess the stability of the modelled structural organization free in solution. To deepen the structural analysis of the C terminal domain, we have also studied the organization of the whole protein inserted into the membrane by a procedure of comparative modeling between fold recognition and folding ab initio. Then, the complete structure of SELK was subjected to MD simulations in the lipid bilayer and a water box. Analyzing the MD trajectories, we found that the C-terminal domain of SELK is still highly mobile during the simulation in water-lipid bilayer by showing a decrease of the structural compactness, a lesser number of H-bonds, as well as a higher value of the total void volume and of the total solvent accessible area compared to the simulation in only water system. However, in both the simulations this region is stabilized mainly by a marked number of H-bonds, and pi-cation and IAC interactions, which suggest a globule organization very different from the classic globular one. Furthermore, water-protein interaction data suggest, as for other IDPs, that the hydration water tends to cluster around the protein facilitating its organization to globule.

Prediction of and Experimental Support for the Three-Dimensional Structure of Replication Protein A

Biochemistry ◽  
2009 ◽  
Vol 48 (33) ◽  
pp. 7892-7905 ◽  
Author(s):  
Jonathan Eric Nuss ◽  
Deacon John Sweeney ◽  
Gerald Michael Alter
Keyword(s):  
Protein A ◽  
Three Dimensional ◽  
Replication Protein A ◽  
Replication Protein ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Experimental Support

Three-Dimensional Structure of Rat Surfactant Protein A Trimers in Association with Phospholipid Monolayers†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (21) ◽  
pp. 6310-6316 ◽  
Author(s):  
Nades Palaniyar ◽  
Francis X. McCormack ◽  
Fred Possmayer ◽  
George Harauz
Keyword(s):  
Protein A ◽  
Three Dimensional ◽  
Surfactant Protein ◽  
Surfactant Protein A ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Phospholipid Monolayers
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