Site-Specific Attachment of a Protein to a Carbon Nanotube End without Loss of Protein Function

2012 ◽  
Vol 23 (7) ◽  
pp. 1488-1493 ◽  
Author(s):  
Shige H. Yoshimura ◽  
Shahbaz Khan ◽  
Satoshi Ohno ◽  
Takashi Yokogawa ◽  
Kazuya Nishikawa ◽  
...  
Keyword(s):  
Carbon Nanotube ◽  
Protein Function ◽  
Site Specific ◽  
Specific Attachment

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

scholarly journals Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function

Small GTPases ◽  
2013 ◽  
Vol 4 (3) ◽  
pp. 186-192 ◽  
Author(s):  
G Aaron Hobbs ◽  
Harsha P Gunawardena ◽  
Rachael Baker ◽  
Xian Chen ◽  
Sharon L Campbell
Keyword(s):  
Protein Function ◽  
Gtpase Activating Protein ◽  
Site Specific

scholarly journals High Conductivity Copper–Carbon Nanotube Hybrids via Site-Specific Chemical Vapor Deposition

2018 ◽  
Vol 2 (1) ◽  
pp. 118-126 ◽  
Author(s):  
Anthony P. Leggiero ◽  
Kylie J. Trettner ◽  
Heather L. Ursino ◽  
Dylan J. McIntyre ◽  
Mark Schauer ◽  
...  
Keyword(s):  
Chemical Vapor Deposition ◽  
Carbon Nanotube ◽  
Vapor Deposition ◽  
Chemical Vapor ◽  
High Conductivity ◽  
Specific Chemical ◽  
Site Specific

Site-Specific Attachment of Proteins onto a 3D DNA Tetrahedron through Backbone-Modified Phosphorothioate DNA

Small ◽  
2011 ◽  
Vol 7 (10) ◽  
pp. 1427-1430 ◽  
Author(s):  
Ngo Yin Wong ◽  
Chuan Zhang ◽  
Li Huey Tan ◽  
Yi Lu
Keyword(s):  
Site Specific ◽  
Specific Attachment ◽  
Dna Tetrahedron

Nano-Structured Beta-Gallia-Rutile Surfaces as Substrates for DNA Self-Assembly

2005 ◽  
Vol 901 ◽  
Author(s):  
Nathan Empie ◽  
Doreen Edwards
Keyword(s):  
Self Assembly ◽  
Divalent Cations ◽  
Dna Adsorption ◽  
Site Specific ◽  
Force Microscopy ◽  
Atomic Force ◽  
Site Selectivity ◽  
Afm Imaging ◽  
Specific Attachment ◽  
Mode Atomic Force Microscopy

AbstractA nano-structured beta-gallia-rutile (BGR) substrate capable of binding DNA was synthesized. Beta-gallia groups diffuse into [001] single crystal rutile along {210}r planes, generating hexagonally shaped tunnel sites between the beta-gallia subunits (repeating ∼1 nm). The tunnel sites, approximately 2.5 Å in diameter, are preferred regions for cation incorporation. Divalent cations have been used previously to adsorb DNA to mica surfaces. For the BGR system, the site selectivity of the cations for tunnel sites could lead to controllable / tailor-able DNA adsorption. DNA buffers containing Cu (II), Fe (II), and Ni (II) cations were deposited on BGR substrates. The DNA adsorption was investigated with tapping mode atomic force microscopy (AFM) to determine the suitability of using BGR substrates as a means to self assemble DNA constructs for nano-electronic applications. At the concentrations tested, only solutions containing Ni (II) ions were capable of binding DNA sufficiently for AFM imaging; there was no evidence of site specific attachment.

scholarly journals Expanding the Zebrafish Genetic Code through Site-Specific Introduction of Azido-lysine, Bicyclononyne-lysine, and Diazirine-lysine

2019 ◽  
Author(s):  
Junetha Syed ◽  
Saravanan Palani ◽  
Scott T. Clarke ◽  
Zainab Asad ◽  
Andrew R. Bottrill ◽  
...  
Keyword(s):  
Genetic Code ◽  
Protein Function ◽  
Fluorescent Protein ◽  
Trna Synthetase ◽  
Glutathione S Transferase ◽  
Base Pairs ◽  
Site Specific ◽  
Green Fluorescent ◽  
Natural Amino Acids ◽  
Sense Codon

AbstractSite-specific incorporation of un-natural amino acids (UNAA) is a powerful approach to engineer and understand protein function [1-4]. Site-specific incorporation of UNAAs is achieved through repurposing the amber codon (UAG) as a sense codon for the UNAA, a tRNACUA that base pairs with an UAG codon in the mRNA and an orthogonal amino-acyl tRNA synthetase (aaRS) that charges the tRNACUA with the UNAA [5, 6]. Here, we report expansion of the zebrafish genetic code to incorporate the UNAAs, Azido-lysine (AzK), bicyclononyne-lysine (BCNK), and Diazirine-lysine (AbK) into green fluorescent protein (GFP) and Glutathione-S-transferase (GST). We also present proteomic evidence for UNAA incorporation into GFP. Our work sets the stage for the use of UNAA mutagenesis to investigate and engineer protein function in zebrafish.

scholarly journals Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jugal Mohapatra ◽  
Kyuto Tashiro ◽  
Ryan L Beckner ◽  
Jorge Sierra ◽  
Jessica A Kilgore ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Protein Function ◽  
Post Translational Modification ◽  
Site Specific ◽  
Precise Control ◽  
Protein Ligation ◽  
Adp Ribosylation ◽  
Nuclear Extracts ◽  
Synthesis Strategy ◽  
The Impact

Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational modification catalyzed by the PARP1/2:HPF1 complex. As the list of PARP1/2:HPF1 substrates continues to expand, there is a need for technologies to prepare mono- and poly-ADP-ribosylated proteins for biochemical interrogation. Here we investigate the unique peptide ADPr activities catalyzed by PARP1 in the absence and presence of HPF1. We then exploit these activities to develop a method that facilitates installation of ADP-ribose polymers onto peptides with precise control over chain length and modification site. Importantly, the enzymatically mono- and poly-ADP-ribosylated peptides are fully compatible with protein ligation technologies. This chemoenzymatic protein synthesis strategy was employed to assemble a series of full-length, ADP-ribosylated histones and show that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates for the chromatin remodeler ALC1. We found ALC1 preferentially remodels 'activated' substrates within heterogeneous mononucleosome populations and asymmetrically ADP-ribosylated dinucleosome substrates, and that nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear extracts. Our study identifies a biochemical function for nucleosome serine ADPr and describes a new, highly modular approach to explore the impact that site-specific serine mono- and poly-ADPr have on protein function.

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