TY - JOUR

T1 - Deciphering the Alphabet of Disorder-Glu and Asp Act Differently on Local but Not Global Properties

AU - Roesgaard, Mette Ahrensback

AU - Lundsgaard, Jeppe E.

AU - Newcombe, Estella A.

AU - Jacobsen, Nina L.

AU - Pesce, Francesco

AU - Tranchant, Emil E.

AU - Lindemose, Søren

AU - Prestel, Andreas

AU - Hartmann-Petersen, Rasmus

AU - Lindorff-Larsen, Kresten

AU - Kragelund, Birthe B.

PY - 2022

Y1 - 2022

N2 - Compared to folded proteins, the sequences of intrinsically disordered proteins (IDPs) are enriched in polar and charged amino acids. Glutamate is one of the most enriched amino acids in IDPs, while the chemically similar amino acid aspartate is less enriched. So far, the underlying functional differences between glutamates and aspartates in IDPs remain poorly understood. In this study, we examine the differential effects of aspartate and glutamates in IDPs by comparing the function and conformational ensemble of glutamate and aspartate variants of the disordered protein Dss1, using a range of assays, including interaction studies, nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and molecular dynamics simulation. First, we analyze the sequences of the rapidly growing database of experimentally verified IDPs (DisProt) and show that glutamate enrichment is not caused by a taxonomy bias in IDPs. From analyses of local and global structural properties as well as cell growth and protein-protein interactions using a model acidic IDP from yeast and three Glu/Asp variants, we find that while the Glu/Asp variants support similar function and global dimensions, the variants differ in their binding affinities and population of local transient structural elements. We speculate that these local structural differences may play roles in functional diversity, where glutamates can support increased helicity, important for folding and binding, while aspartates support extended structures and form helical caps, as well as playing more relevant roles in, e.g., transactivation domains and ion-binding.

AB - Compared to folded proteins, the sequences of intrinsically disordered proteins (IDPs) are enriched in polar and charged amino acids. Glutamate is one of the most enriched amino acids in IDPs, while the chemically similar amino acid aspartate is less enriched. So far, the underlying functional differences between glutamates and aspartates in IDPs remain poorly understood. In this study, we examine the differential effects of aspartate and glutamates in IDPs by comparing the function and conformational ensemble of glutamate and aspartate variants of the disordered protein Dss1, using a range of assays, including interaction studies, nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and molecular dynamics simulation. First, we analyze the sequences of the rapidly growing database of experimentally verified IDPs (DisProt) and show that glutamate enrichment is not caused by a taxonomy bias in IDPs. From analyses of local and global structural properties as well as cell growth and protein-protein interactions using a model acidic IDP from yeast and three Glu/Asp variants, we find that while the Glu/Asp variants support similar function and global dimensions, the variants differ in their binding affinities and population of local transient structural elements. We speculate that these local structural differences may play roles in functional diversity, where glutamates can support increased helicity, important for folding and binding, while aspartates support extended structures and form helical caps, as well as playing more relevant roles in, e.g., transactivation domains and ion-binding.

KW - Dss1

KW - intrinsically disordered protein

KW - IDPs

KW - molecular dynamics

KW - NMR

KW - sequence composition

KW - SAXS

KW - PROTEIN SECONDARY STRUCTURE

KW - FREE-ENERGY LANDSCAPES

KW - INTRINSIC DISORDER

KW - PROTEASOME

KW - EFFICIENT

KW - DYNAMICS

KW - SPECTROSCOPY

KW - PROPENSITY

KW - SCATTERING

KW - PARTICLE

U2 - 10.3390/biom12101426

DO - 10.3390/biom12101426

M3 - Journal article

C2 - 36291634

VL - 12

JO - Biomolecules

JF - Biomolecules

SN - 2218-273X

IS - 10

M1 - 1426

ER -