The challenges of determining metal–protein affinities

2010 ◽  
Vol 27 (5) ◽  
pp. 768 ◽  
Author(s):  
Zhiguang Xiao ◽  
Anthony G. Wedd
Keyword(s):  
Protein Affinities

ChemInform Abstract: The Challenges of Determining Metal-Protein Affinities

ChemInform ◽  
2010 ◽  
Vol 41 (31) ◽  
pp. no-no
Author(s):  
Zhiguang Xiao ◽  
Anthony G. Wedd
Keyword(s):  
Protein Affinities

scholarly journals Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Stephanie Portelli ◽  
Yoochan Myung ◽  
Nicholas Furnham ◽  
Sundeep Chaitanya Vedithi ◽  
Douglas E. V. Pires ◽  
...  
Keyword(s):  
Machine Learning ◽  
Nucleic Acid ◽  
Rna Polymerase ◽  
Gold Standard ◽  
Rifampicin Resistance ◽  
Missense Mutations ◽  
Learning Approaches ◽  
Current Gold Standard ◽  
Sequence Identity ◽  
Protein Affinities

Abstract Rifampicin resistance is a major therapeutic challenge, particularly in tuberculosis, leprosy, P. aeruginosa and S. aureus infections, where it develops via missense mutations in gene rpoB. Previously we have highlighted that these mutations reduce protein affinities within the RNA polymerase complex, subsequently reducing nucleic acid affinity. Here, we have used these insights to develop a computational rifampicin resistance predictor capable of identifying resistant mutations even outside the well-defined rifampicin resistance determining region (RRDR), using clinical M. tuberculosis sequencing information. Our tool successfully identified up to 90.9% of M. tuberculosis rpoB variants correctly, with sensitivity of 92.2%, specificity of 83.6% and MCC of 0.69, outperforming the current gold-standard GeneXpert-MTB/RIF. We show our model can be translated to other clinically relevant organisms: M. leprae, P. aeruginosa and S. aureus, despite weak sequence identity. Our method was implemented as an interactive tool, SUSPECT-RIF (StrUctural Susceptibility PrEdiCTion for RIFampicin), freely available at https://biosig.unimelb.edu.au/suspect_rif/.

scholarly journals High-throughput determination of protein affinities using unmodified peptide libraries in nanomolar scale

iScience ◽  
2021 ◽  
Vol 24 (1) ◽  
pp. 101898
Author(s):  
Clemens Schulte ◽  
Vladimir Khayenko ◽  
Noah Frieder Nordblom ◽  
Franziska Tippel ◽  
Violetta Peck ◽  
...  
Keyword(s):  
High Throughput ◽  
Peptide Libraries ◽  
Unmodified Peptide ◽  
Protein Affinities

scholarly journals Principles and practice of determining metal–protein affinities

2021 ◽  
Vol 478 (5) ◽  
pp. 1085-1116
Author(s):  
Tessa R. Young ◽  
Zhiguang Xiao
Keyword(s):  
Cofactor Binding ◽  
Kd Values ◽  
Probe Selection ◽  
Spectroscopic Probes ◽  
A Cell ◽  
Reliable Quantification ◽  
Regulate Protein ◽  
Protein Affinities ◽  
Selection Of

Metal ions play many critical roles in biology, as structural and catalytic cofactors, and as cell regulatory and signalling elements. The metal–protein affinity, expressed conveniently by the metal dissociation constant, KD, describes the thermodynamic strength of a metal–protein interaction and is a key parameter that can be used, for example, to understand how proteins may acquire metals in a cell and to identify dynamic elements (e.g. cofactor binding, changing metal availabilities) which regulate protein metalation in vivo. Here, we outline the fundamental principles and practical considerations that are key to the reliable quantification of metal–protein affinities. We review a selection of spectroscopic probes which can be used to determine protein affinities for essential biological transition metals (including Mn(II), Fe(II), Co(II), Ni(II), Cu(I), Cu(II) and Zn(II)) and, using selected examples, demonstrate how rational probe selection combined with prudent experimental design can be applied to determine accurate KD values.

scholarly journals Synthesis of Glycodendrimer via Click Chemistry and Protein Affinities

2008 ◽  
Vol 33 (3) ◽  
pp. 729-732 ◽  
Author(s):  
Yoshiko Miura ◽  
Shunsuke Onogi ◽  
Kiyofumi Yamamoto
Keyword(s):  
Click Chemistry ◽  
Protein Affinities

scholarly journals Protein Conformation Ensembles Monitored by HDX Reveal a Structural Rationale for Abscisic Acid Signaling Protein Affinities and Activities

Structure ◽  
2013 ◽  
Vol 21 (2) ◽  
pp. 229-235 ◽  
Author(s):  
Graham M. West ◽  
Bruce D. Pascal ◽  
Ley-Moy Ng ◽  
Fen-Fen Soon ◽  
Karsten Melcher ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Protein Conformation ◽  
Signaling Protein ◽  
Abscisic Acid Signaling ◽  
Protein Affinities

Determination of Transmembrane Protein Affinities for Solutes by Frontal Chromatography

2021 ◽  
pp. 79-93
Author(s):  
Andreas Lundqvist ◽  
Eggert Brekkan ◽  
Lars Haneskog ◽  
Qing Yang ◽  
Jun Miyake ◽  
...  
Keyword(s):  
Transmembrane Protein ◽  
Protein Affinities ◽  
Frontal Chromatography
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