Intrinsic disorder and flexibility in proteins: a challenge for structural biology and drug design

Abstract

The structure–function paradigm, i.e. the concept that it is the three-dimensional structure of a protein that determines its function, has been partially modified by the discovery that a significant portion of the eukaryotic proteome is disordered and that this disorder is often functional. The presence of disorder is the origin of several issues, but the most relevant, at least from the biomedical point of view, is the difficulty of designing drugs in absence of a well-defined conformation of the target. To make the problem worse, we have to consider that often the disorder concerns proteins involved in diseases very relevant for human health, as cancer or neurodegenerative disorders. This review tries to summarize the state of the art of our knowledge on the subject and to describe the tools used to detect disorder and how drug design techniques used for well-folded proteins have been adjusted to this more challenging situation.

Abbreviations: AD: Alzheimer’s disease; CAID: Critical assessment of intrinsic protein disorder; CASP: Critical assessment of protein structure prediction; CD: circular dichroism; Cryo-EM: cryo-electron microscopy; DIBS: differential binding score; FRET: Förster resonance energy transfer; HD: Huntington’s disease; IDR: Intrinsically disordered regions; IDP: intrinsically disordered proteins; LDR: long intrinsically disordered regions; MG: Molten globule; MoRF: Molecular recognition feature; NMR: Nuclear magnetic resonance; PDB: Protein Data Bank; PD: Parkinson’s disease; POMS: polyoxometalates; SAXS: Small-angle X-ray scattering; SLiMS: short linear motifs; TFs: Transcription factors.

KEYWORDS:

• Intrinsically disordered protein
• Intrinsically disordered regions
• Three-dimensional structures
• Flexibility
• Conformations
• drug design
• protein complexes

Acknowledgements

This paper is not founded by a specific grant, but I have to express my gratitude to all brilliant students and people that collaborated with me during my long scientific career. They cannot be listed here, otherwise these acknowledgments would be longer than the paper itself.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Subject Index

active-site directed regulation 59

Aβ42 65

Aducanumab 65

Afatinib 63

Allosteric mechanism 58

AlphaFold 55, 56, 62

Alzheimer’s disease (AD) 63

amyotrophic lateral sclerosis 63

α-synuclein 64

B factors 52, 53

β-catenin 62, 63

BMRB 55

CASP 56

CAID 56

chameleonic sequences 49

Charcot–Marie–Tooth diseases 63

c-MYC  63

circular dichroism spectroscopy (CD) 54

Condensate 60

conformational flexibility 50

Cryo-electron microscopy (cryo-EM) 55

denatured state 49

DIBS 54

disorder-to-order transition 51, 58

DisProt 53

DisResClusteredDB 53

dynamic behaviour 50

ELIXIR  54

ELM 54

eukaryotic protein 49, 52

flexible or disordered regions 52, 55

flexibility 49, 50, 52, 63, 65

FLIPPER 53

frontotemporal dementia 63

FRET 54, 55, 56

fully folded structure 49

FuzDB 54

High specificity 57

hydrophobic residues 52

hydrophilic surface 52

hydrodynamic radius 52

Huntington’s disease (HD) 63

Ibrutinib 63

IDEAL  53

In silico design 60

interdomain allostery 58

intramolecular regulation 58

intrinsically disordered proteins 50, 51

intrinsically disordered regions 51, 53

Lewy bodies 64

long intrinsically disordered regions 53

Low affinity 61

MAX 62, 63

metamorphic states 49

MFIB 54

missing residues 52, 54

mitochondrial myopathy 63

MobiDB 53

molten globule state 49

moonlighting proteins  49

MoonProt 55

MOREs 59

MORFs 59

morpheeins 49

NMR 51, 54, 55, 56, 59

on-off mechanism 50

Parkinson’s disease (PD) 63

PDB 49, 50, 51, 52

PED 54

phosphorylation site 50

Phosphotyrosine 62

phyla 50

PolyX, polyXY 57

post-translational modifications 52

pre-molten globule state 49

prion like 64

protein-DNA complexes 59

protein complexes 53

Prothymosin- α 58

random coil 49

Random conformation 49, 50

Sar1-GTP 53

Sec23/2 53

Sec13/31 53

signalling conduit function 59

single crystal electron diffraction 55

SH2B1 60

SLiMS 58

Small-angle X-ray scattering (SAXS) 54, 56

spinal muscular atrophy 63

STAT3 61

structure–function relationship 49

structural heterogeneity 52

TATA-binding protein 60

TBP-associated factors 60

Tcf 63

TFIID 60

TFs 61, 63

thermal parameters 52

unfolded 49, 50, 51, 60

UniProtKB 54

vibrational Raman optical activity 56

Wnt signalling pathway 63

X-ray powder diffraction 55

Additional information

Notes on contributors

Giuseppe Zanotti

Giuseppe Zanotti was Full Professor of chemistry and then of Biochemistry at the University of Padova, Italy, before his retirement in October 2021. Since the beginning of his scientific career, he has been active in the field of structural biology, mostly using X-ray diffraction and, more recently, cryo-Electron Microscopy. He has been interested in proteins that bind and transport small hydrophobic molecules, of protein kinase CK2/inhibitor complexes and of proteins from pathogenic bacteria, in particular Helicobacter pylori. More recently he moved to the structure of filamentous viruses and protein complexes by cryo-EM. He has also been interested in theoretical aspects of macromolecular structures and has proposed the use of tensegrity as a unifying concept of protein folds. More information at the Blog https://sofiaelamela.com.