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List of works by Andrei N. Lupas

A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels

scientific article

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

scientific article published on 16 December 2017

A Trimeric Lipoprotein Assists in Trimeric Autotransporter Biogenesis in Enterobacteria

scientific article published on 14 March 2014

A coiled-coil motif that sequesters ions to the hydrophobic core

scientific article

A conserved glycine residue of trimeric autotransporter domains plays a key role in Yersinia adhesin A autotransport

scientific article published on 5 October 2007

A domain dictionary of trimeric autotransporter adhesins

scientific article

A galaxy of folds

scientific article published on January 2010

A new expression system for protein crystallization using trimeric coiled-coil adaptors

scientific article

A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity

scientific article

A topological refactoring design strategy yields highly stable granulopoietic proteins

scientific article published on 26 May 2022

A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins

scientific article

A vocabulary of ancient peptides at the origin of folded proteins

scientific article

AAA proteins

scientific article

AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels

scientific article

Adenylate cyclases: Receivers, transducers, and generators of signals.

scientific article

An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture

article by Mohammad ElGamacy et al published 27 August 2018 in ACS Synthetic Biology

An endosomal tether undergoes an entropic collapse to bring vesicles together

scientific article

Asymmetric protein design from conserved supersecondary structures

scientific article published on 26 October 2018

Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding

scientific article published on 13 November 2019

Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor

scientific article

Barentsz, a new component of the Staufen-containing ribonucleoprotein particles in mammalian cells, interacts with Staufen in an RNA-dependent manner

scientific article (publication date: 2 July 2003)

Bartonella adhesin a mediates a proangiogenic host cell response

scientific article

Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation

scientific article

Bioinformatics of the TULIP domain superfamily

scientific article published on August 2011

CLANS: a Java application for visualizing protein families based on pairwise similarity

scientific article published on 29 July 2004

Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea

scientific article

Characterization of a novel signal transducer element intrinsic to class IIIa/b adenylate cyclases and guanylate cyclases

scientific article published on 21 February 2017

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation

scientific article published on 20 November 2017

Chemical Ligand Space of Cereblon

scientific article published on 14 September 2018

Classification of AAA+ proteins

scientific article published on 26 May 2006

Coiled Coils - A Model System for the 21st Century

scientific article published on 21 November 2016

Coiled coils meet the chaperone world

scientific article published in September 2004

Common evolutionary origin of swapped-hairpin and double-psi beta barrels

scientific article

Comparative analysis of coiled-coil prediction methods

scientific article published on 31 March 2006

Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria

scientific article

Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction

scientific article

Correction: β-Propeller Blades as Ancestral Peptides in Protein Evolution.

scientific article

Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.

scientific article

Crystal structure of SpoVT, the final modulator of gene expression during spore development in Bacillus subtilis

scientific article

Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor

scientific article

Crystallographic snapshot of the Escherichia coli EnvZ histidine kinase in an active conformation

scientific article

Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII.

scientific article published on 20 June 2012

Design of novel granulopoietic proteins by topological rescaffolding

scientific article published on 22 December 2020

Domain annotation of trimeric autotransporter adhesins--daTAA

scientific article

Editorial

Evolution of the beta-propeller fold

scientific article published in May 2008

Evolutionary relationships of microbial aromatic prenyltransferases

scientific article

Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli

scientific article

Fold recognition without folds

scientific article

From ancestral peptides to designed proteins

scientific article

Functional mapping of YadA- and Ail-mediated binding of human factor H to Yersinia enterocolitica serotype O:3.

scientific article published on 2 September 2008

Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels

scientific article

HAMP Domain-mediated Signal Transduction Probed with a Mycobacterial Adenylyl Cyclase as a Reporter ⬇️

scientific article published on November 17, 2011

HHomp--prediction and classification of outer membrane proteins

scientific article

HHsenser: exhaustive transitive profile search using HMM-HMM comparison

scientific article published on July 2006

Histones predate the split between bacteria and archaea

scientific article published on 01 July 2019

Historical review: another 50th anniversary--new periodicities in coiled coils

scientific article published on December 2003

Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria

scientific article published on 16 June 2010

Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases

scientific article published on April 2007

Journal of Structural Biology - Paper of the Year 2017.

scientific article published on 30 January 2018

Measuring the conformational space of square four-helical bundles with the program samCC.

scientific article published on 6 February 2010

Mechanism of regulation of receptor histidine kinases

scientific article

Model structure of the prototypical non-fimbrial adhesin YadA of Yersinia enterocolitica

scientific article

Modeling AAA+ ring complexes from monomeric structures

scientific article published on 7 May 2006

More than the sum of their parts: on the evolution of proteins from peptides

scientific article

On the origin of the histone fold

scientific article

Origin of a folded repeat protein from an intrinsically disordered ancestor

scientific article

PhyloGenie: automated phylome generation and analysis

scientific article published on 30 September 2004

Phylogenetic analysis of AAA proteins

scientific article

PrlF and YhaV form a new toxin-antitoxin system in Escherichia coli

scholarly article published April 2006

Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis

scientific article published on 9 December 2013

Protein Design. What I cannot create, I do not understand

scientific article published in December 2014

Purification of the YadA membrane anchor for secondary structure analysis and crystallization

scientific article

REPPER--repeats and their periodicities in fibrous proteins

scientific article

Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins

scientific article

SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay

scientific article

STAC--A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems

scientific article

Salmonella Pathogenicity Island 4 encodes a giant non-fimbrial adhesin and the cognate type 1 secretion system

scientific article published on 26 March 2007

Some of the most interesting CASP11 targets through the eyes of their authors

scientific article

Structural diversity of oligomeric β-propellers with different numbers of identical blades

scientific article published on 15 October 2019

Structural dynamics of the cereblon ligand binding domain

scientific article published on 29 May 2015

Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases

scientific article

Structure and evolution of N-domains in AAA metalloproteases

scientific article

Structure and function of tripeptidyl peptidase II, a giant cytosolic protease ⬇️

scientific article published on July 13, 2011

Structure of the head of the Bartonella adhesin BadA

scientific article published in 2008

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

scientific article

The GD box: a widespread noncontiguous supersecondary structural element

scientific article

The HAMP domain structure implies helix rotation in transmembrane signaling

scientific article

The HHpred interactive server for protein homology detection and structure prediction

scientific article

The MPI Bioinformatics Toolkit for protein sequence analysis

scientific article published on July 2006

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

scientific article

The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment

scientific article published in 2018

The Structure and Topology of α-Helical Coiled Coils

scientific article published on January 2017

The Sulfolobus solfataricus AAA protein Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase

scientific article published in February 2008

The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport

scientific article published on 26 January 2016

The archaeal proteasome is regulated by a network of AAA ATPases

scientific article

The breakthrough in protein structure prediction

scientific article published in 2021

The first prokaryotic trehalose synthase complex identified in the hyperthermophilic crenarchaeon Thermoproteus tenax

scientific article

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum

scientific article

The head of Bartonella adhesin A is crucial for host cell interaction of Bartonella henselae

scientific article

The long coming of computational structural biology.

scientific article

The mechanisms of HAMP-mediated signaling in transmembrane receptors

scientific article

The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric autotransporter adhesins

scientific article

The structure of alpha-helical coiled coils

scientific article

The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the β-tent fold

scientific article

Thermoplasma acidophilum TAA43 is an archaeal member of the eukaryotic meiotic branch of AAA ATPases.

scientific article

Trimeric autotransporter adhesins: variable structure, common function

scientific article

Two unique membrane-bound AAA proteins from Sulfolobus solfataricus

scientific article published in February 2009

WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy

scientific article

prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli

scientific article published on 21 July 2007

α/β coiled coils

scientific article published on 15 January 2016

β-Propeller blades as ancestral peptides in protein evolution

scientific article

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