Protein intrinsic disorder and induced pluripotent stem cells

Intrinsically disordered proteins may escape unwanted interactions via functional misfolding

(2011) Vladimir N. Uversky   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Disorder Targets Misorder in Nuclear Quality Control Degradation: A Disordered Ubiquitin Ligase Directly Recognizes Its Misfolded Substrates

(2011) Joel C. Rosenbaum et al.   MOLECULAR CELL

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

(2010) Bin Xue et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Flexible Nets of Malleable Guardians: Intrinsically Disordered Chaperones in Neurodegenerative Diseases

(2010) Vladimir N. Uversky   CHEMICAL REVIEWS

Induced pluripotent stem cells: what lies beyond the paradigm shift

(2010) Jesse L Cox et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

SPA: Short peptide analyzer of intrinsic disorder status of short peptides

(2010) Bin Xue et al.   GENES TO CELLS

Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction

(2010) Bin Xue et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins

(2010) Justin Yamada et al.   MOLECULAR & CELLULAR PROTEOMICS

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes

(2010) Prasad V. Burra et al.   PLoS One

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Collaboration between WNT and BMP signaling promotes hemoangiogenic cell development from human fibroblast-derived iPS cells

(2010) Yi Wang et al.   Stem Cell Research

The Interplay of Catalysis and Toxicity by Amyloid Intermediates on Lipid Bilayers: Insights from Type II Diabetes

(2009) James A. Hebda et al.   Annual Review of Biophysics

Structural Polymorphism and Multifunctionality of Myelin Basic Protein

(2009) George Harauz et al.   BIOCHEMISTRY

Functionalization of a nanopore: The nuclear pore complex paradigm

(2009) Reiner Peters   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Close encounters of the third kind: disordered domains and the interactions of proteins

(2009) Peter Tompa et al.   BIOESSAYS

ANCHOR: web server for predicting protein binding regions in disordered proteins

(2009) Z. Dosztanyi et al.   BIOINFORMATICS

Predicting intrinsic disorder in proteins: an overview

(2009) Bo He et al.   CELL RESEARCH

Limitations of Induced Folding in Molecular Recognition by Intrinsically Disordered Proteins

(2009) Eszter Hazy et al.   CHEMPHYSCHEM

Biophysical characterization of intrinsically disordered proteins

(2009) David Eliezer   CURRENT OPINION IN STRUCTURAL BIOLOGY

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mouse ZAR1-like (XM_359149) colocalizes with mRNA processing components and its dominant-negative mutant caused two-cell-stage embryonic arrest

(2009) Jianjun Hu et al.   DEVELOPMENTAL DYNAMICS

A tale of two tails: Activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1

(2009) Vasundhara M. Navadgi-Patil et al.   DNA REPAIR

Dynamic interactions of proteins in complex networks: a more structured view

(2009) Amelie Stein et al.   FEBS Journal

CDF it all: Consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions

(2009) Bin Xue et al.   FEBS LETTERS

Roles of Sall4 in the generation of pluripotent stem cells from blastocysts and fibroblasts

(2009) Noriko Tsubooka et al.   GENES TO CELLS

Linking the p53 tumour suppressor pathway to somatic cell reprogramming

(2009) Teruhisa Kawamura et al.   NATURE

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity

(2009) Rosa M. Marión et al.   NATURE

Suppression of induced pluripotent stem cell generation by the p53–p21 pathway

(2009) Hyenjong Hong et al.   NATURE

Immortalization eliminates a roadblock during cellular reprogramming into iPS cells

(2009) Jochen Utikal et al.   NATURE

Embryonic stem cell–specific microRNAs promote induced pluripotency

(2009) Robert L Judson et al.   NATURE BIOTECHNOLOGY

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

(2009) Bo Feng et al.   NATURE CELL BIOLOGY

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The rules of disorder or why disorder rules

(2009) Jörg Gsponer et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Intrinsically Disordered Proteins and Their Environment: Effects of Strong Denaturants, Temperature, pH, Counter Ions, Membranes, Binding Partners, Osmolytes, and Macromolecular Crowding

(2009) Vladimir N. Uversky   PROTEIN JOURNAL

Modularity of intrinsic disorder in the human proteome

(2009) Melissa M. Pentony et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Regulation of Stem Cell Pluripotency and Differentiation Involves a Mutual Regulatory Circuit of the Nanog, OCT4, and SOX2 Pluripotency Transcription Factors With Polycomb Repressive Complexes and Stem Cell microRNAs

(2009) Vasundhra Kashyap et al.   STEM CELLS AND DEVELOPMENT

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

(2009) Malene Ringkjøbing Jensen et al.   STRUCTURE

Regulatory circuits underlying pluripotency and reprogramming

(2009) Jeong Tae Do et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors

(2009) Satoshi Fukuchi et al.   BMC STRUCTURAL BIOLOGY

Prediction of Protein Binding Regions in Disordered Proteins

(2009) Bálint Mészáros et al.   PLoS Computational Biology

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

(2008) Vladimir N. Uversky et al.   Annual Review of Biophysics

Regulation of Cell Division by Intrinsically Unstructured Proteins: Intrinsic Flexibility, Modularity, and Signaling Conduits†

(2008) Charles A. Galea et al.   BIOCHEMISTRY

N-Myc Regulates a Widespread Euchromatic Program in the Human Genome Partially Independent of Its Role as a Classical Transcription Factor

(2008) R. Cotterman et al.   CANCER RESEARCH

Disease-Specific Induced Pluripotent Stem Cells

(2008) In-Hyun Park et al.   CELL

The Growth Factor Environment Defines Distinct Pluripotent Ground States in Novel Blastocyst-Derived Stem Cells

(2008) Yu-Fen Chou et al.   CELL

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

c-Myc Is Dispensable for Direct Reprogramming of Mouse Fibroblasts

(2008) Marius Wernig et al.   Cell Stem Cell

Wnt Signaling Promotes Reprogramming of Somatic Cells to Pluripotency

(2008) Alexander Marson et al.   Cell Stem Cell

Having it both ways: Sox protein function between conservation and innovation

(2008) S. I. E. Guth et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Sex determination in mammals — Before and after the evolution of SRY

(2008) M. C. Wallis et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Function and structure of inherently disordered proteins

(2008) A Keith Dunker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A careful disorderliness in the proteome: Sites for interaction and targets for future therapies

(2008) Robert B. Russell et al.   FEBS LETTERS

Pluripotent stem cell lines

(2008) J. Yu et al.   GENES & DEVELOPMENT

Role of Backbone−Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Proteins

(2008) Hoang T. Tran et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Role of intrinsically disordered protein regions/domains in transcriptional regulation

(2008) Anna S. Garza et al.   LIFE SCIENCES

Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes

(2008) Amrita Mohan et al.   Molecular BioSystems

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Malleable machines take shape in eukaryotic transcriptional regulation

(2008) Monika Fuxreiter et al.   Nature Chemical Biology

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

(2008) Andrew Campen et al.   PROTEIN AND PEPTIDE LETTERS

Fuzzy complexes: polymorphism and structural disorder in protein–protein interactions

(2007) Peter Tompa et al.   TRENDS IN BIOCHEMICAL SCIENCES