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Metal Binding in Proteins: Machine Learning Complements X-Ray Absorption Spectroscopy [chapter]

Marco Lippi, Andrea Passerini, Marco Punta, Paolo Frasconi
2012 Lecture Notes in Computer Science  
We present an application of machine learning algorithms for the identification of metalloproteins and metal binding sites on a genome scale.  ...  An extensive evaluation conducted in combination with Xray absorption spectroscopy shows the great potentiality of the approach.  ...  High-throughput techniques based on X-ray absorption spectroscopy [3] (HT-XAS) allow detection, identification and quantification of metals bound to proteins based on the energy and intensity of the  ... 
doi:10.1007/978-3-642-33486-3_63 fatcat:v4aztoo2ajdqxhjobwupi6itpy

Exploiting 3D structural templates for detection of metal-binding sites in protein structures

Kshama Goyal, Shekhar C. Mande
2007 Proteins: Structure, Function, and Bioinformatics  
It then scans all the available protein structures in the PDB database for putative metal-binding sites.  ...  Prediction of metal-binding site in a yeast protein YDR533c led to the hypothesis that it might function as metal-dependent amidopeptidase.  ...  Gowrishankar in this work. We would like to thank N. Srinivasan and D. Mohanty for their valuable suggestions and encouraging discussions. Yashaswini Kandan is acknowledged for useful ideas.  ... 
doi:10.1002/prot.21601 pmid:17847089 fatcat:mgq5t3n3tzafllnamfm6wkqwmq

Predicting Metal-Binding Sites from Protein Sequence

A. Passerini, M. Lippi, P. Frasconi
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We develop new algorithmic ideas based on structuredoutput learning for determining transition-metal-binding sites coordinated by cysteines and histidines.  ...  Prediction of binding sites from sequence can significantly help toward determining the function of uncharacterized proteins on a genomic scale.  ...  In recent years, high-throughput experimental techniques based on X-ray absorption spectroscopy [8] , [9] , [10] proved capable of identifying metalloproteins with high reliability.  ... 
doi:10.1109/tcbb.2011.94 pmid:21606549 fatcat:subasuglynazbpyqwd2qrcbdba

Technologies for the identification and validation of protein-protein interactions

Karoline Pichlerova, Jozef Hanes
2021 General Physiology and Biophysics  
Proteins are large molecules that play essential roles in all living organisms.  ...  In most molecular processes in each cell, proteins usually do not function alone but through physiological interactions with various ligands.  ...  In silico methods are based on either statistical assumptions or machine learning, and are applied to protein sequences, structures or whole databases.  ... 
doi:10.4149/gpb_2021035 pmid:34897023 fatcat:nql5wdtghjbbnpsy7oizl7d43a

Protein folding by NMR

Anastasia Zhuravleva, Dmitry M. Korzhnev
2017 Progress in nuclear magnetic resonance spectroscopy  
RF -radiofrequency RNC -ribosome-nascent chain SAXSsmall angle X-ray scattering SBD -substrate-binding domain SSP -secondary structure propensity ST -saturation transfer SUV -small unilamellar liposome  ...  Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes  ...  Research in DMK lab is supported by NSF MCB (1615866).  ... 
doi:10.1016/j.pnmrs.2016.10.002 pmid:28552172 fatcat:3ooryri6cfedxc3tjvse2wwave

Computational approaches for de novo design and redesign of metal-binding sites on proteins

Gunseli Bayram Akcapinar, Osman Ugur Sezerman
2017 Bioscience Reports  
Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins.  ...  Metal ions play pivotal roles in protein structure, function and stability.  ...  the bound metal ion since current high-throughput methods based on X-ray absorption spectroscopy can only identify its presence but cannot identify the residues involved in metal ion binding [28, 29]  ... 
doi:10.1042/bsr20160179 pmid:28167677 pmcid:PMC5482196 fatcat:7oanpxahqveopmijnciatqmqfi

Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy

W. Shi, M. Punta, J. Bohon, J. M. Sauder, R. D'Mello, M. Sullivan, J. Toomey, D. Abel, M. Lippi, A. Passerini, P. Frasconi, S. K. Burley (+2 others)
2011 Genome Research  
High-throughput X-ray absorption spectroscopy was used to measure transition metal content based on quantitative detection of X-ray fluorescence signals for 3879 purified proteins from several hundred  ...  As the HT-XAS identifies metal type and protein binding, while the bioinformatics analysis identifies metal-binding residues, the results were combined to identify putative metal-binding sites in the proteins  ...  HT-XAS employs the physical principle of X-ray excitation of core electrons of metal atoms with detection of resulting X-ray fluorescence as in X-ray absorption spectroscopy (Shi et al. 2005) .  ... 
doi:10.1101/gr.115097.110 pmid:21482623 pmcid:PMC3106322 fatcat:zzcv5nwisbczvaowbpr3llcwni

Abstracts of the 29th Annual Symposium of The Protein Society

2015 Protein Science  
In this work, we describe the isolation, selection and characterization of a bacterial system capable of regulated, extracellular biosynthesis of metal sulfide QDs with extrinsic control over nanocrystal  ...  The interactions of SPM-1 with various potential inhibitors were reported by 19F-NMR, which enabled monitoring SPM-1 conformational changes on ligand binding and informed on binding strength by enabling  ...  Protein Structural Biology Structural and functional investigation of the far C-terminal domain (CTD) of the bifunctional enzyme TraI using NMR Spectroscopy B.Krishna Chaitanya, Evelyne Schrank and Klaus  ... 
doi:10.1002/pro.2823 pmid:26452528 pmcid:PMC4632850 fatcat:ejmksoqj3zbsrkabl4jyp7emgi

Research progress and application opportunities of nanoparticle–protein corona complexes

Wei Huang, Gao Xiao, Yujuan Zhang, Weiping Min
2021 Biomedicine and Pharmacotherapy  
The discovery of the presence of protein corona (PC) has changed our classical view of NPs, stimulating researchers to investigate the in vivo fate of NPs as they enter biological systems.  ...  Both NPs and PC have their specificity but complement each other, so they should be considered as a whole.  ...  Moreover, small-angle X-ray scattering (SAXS) can be used to measure the particles with the sizes in the range of 1-100 nm, especially ranging from 5 to 25 nm [29] .  ... 
doi:10.1016/j.biopha.2021.111541 pmid:33848776 fatcat:mcnelcjsabaonjabhlqidpduge

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

Bruno Villoutreix, Karine Bastard, Olivier Sperandio, Robin Fahraeus, Jean-Luc Poyet, Fabien Calvo, Benoit Deprez, Maria Miteva
2008 Current Pharmaceutical Biotechnology  
Different in silico methods have been developed to analyze the physical properties of proteins and learn more about how these properties are associated with binding.  ...  Protein-protein interface: a brief overview Proteins are usually involved in interactions with an estimated average of 5-10 protein partners [41] , the binding site(s) with these partners may or may not  ...  Several protein-protein interactions have been successfully targeted using chemistry-in silico-in vitro screening approaches (and other biophysical methods such X-ray crystallography [258, 259] or NMR  ... 
doi:10.2174/138920108783955218 pmid:18393867 fatcat:db63x2enijagzdo34ttc4hqshy

The 28th Annual Symposium of The Protein Society: Program & Abstracts

2014 Protein Science  
Successfully engineered tetrahedrally-shaped protein cages (16 nm in diameter) were verified by x-ray crystallography, small-angle x-ray scattering and electron microscopy.  ...  Data obtained from analytical ultracentrifugation, small-angle X-ray scattering and X-ray crystallography will be included.  ...  Since their discovery, knotted proteins have become an area of exciting study in protein folding.  ... 
doi:10.1002/pro.2504 pmid:25043257 pmcid:PMC4116645 fatcat:yjhug3aif5futn3icovvrkgebm

Reactive molecular dynamics: From small molecules to proteins

Markus Meuwly
2018 Zenodo  
Both, methodological aspects and applications to problems ranging from gas phase reaction dynamics to ligand‐binding in solvated proteins are discussed, focusing on extracting information from simulations  ...  Both, merits and shortcomings of the various methods are discussed and the outlook summarizes possible future avenues such as reactive potentials based on machine learning techniques.  ...  MM thanks all current and previous group members as indicated in the references for their contributions to bring the study of reactive processes using empirical force fields forward.  ... 
doi:10.5281/zenodo.3701316 fatcat:bz2qswg3dbajne2vsfcphwhad4

Liprotides: a New Class of Protein Lipid-Complexes

Jannik N. Pedersen, Henriette Kristina S. Frislev, Jan S. Pedersen, Daniel E. Otzen
2016 Biophysical Journal  
The optical design of the beamline and the results from x-ray tracing simulation [2] are discussed. The source is an in-vacuum undulator with 2 m magnetic length.  ...  All modern hard X-ray synchrotron facilities are promoting the upgrade or the development of SAXS beamlines [1].  ...  The morphological characterization is complemented by X-ray reflectivity and electron microscopy.  ... 
doi:10.1016/j.bpj.2015.11.3085 fatcat:eqeeb47atfc4lisnurb25n55gu

Membrane protein structural insights from chemical labeling and mass spectrometry

Yan Pan, Lars Konermann
2010 The Analyst  
The combination of pulsed oxidative labeling and stopped-flow spectroscopy provided key iii 3 structural insights into the kinetic mechanism by which the SDS-denatured protein inserts and folds into the  ...  Isotope exchange was found to be much faster during light exposure than in the dark.  ...  Around 85% of the protein structures available in the PDB were determined by X-ray crystallography. X-ray crystallography can solve the structures of very large molecules.  ... 
doi:10.1039/b924805f pmid:20498872 fatcat:nb5ofijasre6ldoxnldsgdqlgu

Engineering stable carbonic anhydrases for CO2 capture: a critical review

Mirfath Sultana Mesbahuddin, Aravindhan Ganesan, Subha Kalyaanamoorthy, Roberto Chica
2021 Protein Engineering Design & Selection  
Targeted inhibition of misregulated proteinprotein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases.  ...  The strategies described here can be explored for other proteinprotein interactions and aid in designing new libraries or improving on previous libraries.  ...  This research was undertaken thanks in part to funding from the New Frontiers Research Fund (NFRF) Exploration Award (NFRFE-2019-01339).  ... 
doi:10.1093/protein/gzab021 pmid:34427656 fatcat:zynkqrkbz5guxnrtvijg3lb64y
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