Protein structure predictions articles within Nature Communications

Featured

• Article
  04 December 2020 | Open Access

  Integrative modeling of membrane-associated protein assemblies

  Most approaches for modeling the membrane protein complexes are not capable of incorporating the topological information provided by the membrane. Here authors present an integrative computational protocol for the modeling of membrane-associated protein assemblies, specifically complexes consisting of a membrane-embedded protein and a soluble partner.

  • Jorge Roel-Touris
  • , Brian Jiménez-García
  •  & Alexandre M. J. J. Bonvin

• Article
  20 November 2020 | Open Access

  Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

  Identifying variants capable of causing genetic disease is challenging. The authors use semisupervised learning to predict pathogenic missense variants and their impacts on protein structure and function, enabling a molecular mechanism-driven approach to studying different types of human disease.

  • Vikas Pejaver
  • , Jorge Urresti
  •  & Predrag Radivojac

• Article
  17 October 2019 | Open Access

  Transforming protein-polymer conjugate purification by tuning protein solubility

  Therapeutic proteins are often conjugated with polymers, but separating the conjugate from unconjugated protein and free polymer is a major challenge. Here, the authors discover that proteins conjugated to charged or zwitterionic polymers maintain solubility in 100% ammonium sulfate, greatly simplifying purification.

  • Stefanie L. Baker
  • , Aravinda Munasinghe
  •  & Alan J. Russell

• Article
  04 September 2019 | Open Access

  Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

  Prediction of protein structures on the scale of genomes remains a challenge. Here the authors introduce a protein structure prediction method that uses deep learning to predict inter-atomic distances, torsion angles and hydrogen bonds, and apply it to predict the structures of 1475 Pfam domains.

  • Joe G. Greener
  • , Shaun M. Kandathil
  •  & David T. Jones

• Article
  15 July 2019 | Open Access

  Environmental conditions shape the nature of a minimal bacterial genome

  Minimal bacterial genomes still contain hundreds of genes of unknown function. Here the authors use in silico annotation methods and identify the environmental factors shaping a minimal genome.

  • Magdalena Antczak
  • , Martin Michaelis
  •  & Mark N. Wass

• Article
  14 January 2019 | Open Access

  Rapid determination of quaternary protein structures in complex biological samples

  Protein structure determination in complex biological samples is still challenging. Here, the authors develop a computational modeling-guided cross-linking mass spectrometry method, obtaining a high-resolution model of a 1.8 MDa protein assembly from cross-links detected in a mixture of human plasma and bacteria.

  • Simon Hauri
  • , Hamed Khakzad
  •  & Lars Malmström

• Article
  26 January 2018 | Open Access

  Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra

  Further automation of NMR structure determination is needed to increase the throughput and accessibility of this method. Here the authors present 4D-CHAINS/autoNOE-Rosetta, a complete pipeline that allows rapid and fully automated structure determination from two highly complementary NMR datasets.

  • Thomas Evangelidis
  • , Santrupti Nerli
  •  & Konstantinos Tripsianes

• Article
  09 November 2016 | Open Access

  MHC class II complexes sample intermediate states along the peptide exchange pathway

  MHCII proteins bind and present both foreign and self-antigens to potentially activate CD4+ T cells via cognate T cell receptors (TCRs) during the adaptive immune response. Here, the authors combine NMR-detected H/D exchange with Markov modelling analysis to shed light on the dynamics of MHCII peptide exchange.

  • Marek Wieczorek
  • , Jana Sticht
  •  & Christian Freund

• Article
  03 October 2016 | Open Access

  Dimerization deficiency of enigmatic retinitis pigmentosa-linked rhodopsin mutants

  Retinitis pigmentosa is often caused by mutations that affect the activity or transport of rhodopsin, but some mutations cause disease even though an apparently functional protein is produced. Here the authors show that three such enigmatic mutants retain scramblase activity but are unable to dimerize.

  • Birgit Ploier
  • , Lydia N. Caro
  •  & Anant K. Menon

• Article
  31 August 2016 | Open Access

  Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

  Protein conformational changes are key to a wide range of cellular functions but remain difficult to access experimentally. Here the authors describe eBDIMS, a novel approach to predict intermediates observed in structural transition pathways from experimental ensembles.

  • Laura Orellana
  • , Ozge Yoluk
  •  & Erik Lindahl

• Article
  26 August 2016 | Open Access

  Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

  Allostery is a key molecular mechanism underpinning control and modulation in a variety of cellular processes. Here, the authors present a method that can be used to predict allosteric sites and the mediating interactions that connect them to the active site of the protein.

  • B. R. C. Amor
  • , M. T. Schaub
  •  & M. Barahona

• Article | 21 May 2015

  Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy

  While the transmembrane regions of single-pass transmembrane proteins play critical roles in receptor signalling, they remain difficult to characterize structurally. Here the authors present a computational approach for accurate structure prediction of associated single-pass transmembrane helical proteins.

  • Y. Wang
  •  & P. Barth