Liquid-Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins

Liquid-liquid phase separation of flexible biomolecules has been identified as a ubiquitous phenomenon underlying the formation of membraneless organelles that harbor a multitude of essential cellular processes. We use nuclear magnetic resonance (NMR) spectroscopy to compare the dynamic properties of an intrinsically disordered protein (measles virus N_TAIL) in the dilute and dense phases at atomic resolution. By measuring ¹⁵N NMR relaxation at different magnetic field strengths, we are able to characterize the dynamics of the protein in dilute and crowded conditions and to compare the amplitude and timescale of the different motional modes to those present in the membraneless organelle. Although the local backbone conformational sampling appears to be largely retained, dynamics occurring on all detectable timescales, including librational, backbone dihedral angle dynamics and segmental, chainlike motions, are considerably slowed down. Their relative amplitudes are also drastically modified, with slower, chain-like motions dominating the dynamic profile. In order to provide additional mechanistic insight, we performed extensive molecular dynamics simulations of the protein under self-crowding conditions at concentrations comparable to those found in the dense liquid phase. Simulation broadly reproduces the impact of formation of the condensed phase on both the free energy landscape and the kinetic interconversion between states. In particular, the experimentally observed reduction in the amplitude of the fastest component of backbone dynamics correlates with higher levels of intermolecular contacts or entanglement observed in simulations, reducing the conformational space available to this mode under strongly self-crowding conditions.

Structural insights into p300 regulation and acetylation-dependent genome organisation

Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.

Convergent views on disordered protein dynamics from NMR and computational approaches

Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide 15N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important.

NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins

Intrinsically disordered proteins are ubiquitous throughout all known proteomes, playing essential roles in all aspects of cellular and extracellular biochemistry. To understand their function, it is necessary to determine their structural and dynamic behavior and to describe the physical chemistry of their interaction trajectories. Nuclear magnetic resonance is perfectly adapted to this task, providing ensemble averaged structural and dynamic parameters that report on each assigned resonance in the molecule, unveiling otherwise inaccessible insight into the reaction kinetics and thermodynamics that are essential for function. In this review, we describe recent applications of NMR-based approaches to understanding the conformational energy landscape, the nature and time scales of local and long-range dynamics and how they depend on the environment, even in the cell. Finally, we illustrate the ability of NMR to uncover the mechanistic basis of functional disordered molecular assemblies that are important for human health.

Visualizing protein breathing motions associated with aromatic ring flipping

Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold1-3. It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1. However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa.

The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a

The processes of genome replication and transcription of SARS-CoV-2 represent important targets for viral inhibition. Betacoronaviral nucleoprotein (N) is a highly dynamic cofactor of the replication-transcription complex (RTC), whose function depends on an essential interaction with the amino-terminal ubiquitin-like domain of nsp3 (Ubl1). Here, we describe this complex (dissociation constant - 30 to 200 nM) at atomic resolution. The interaction implicates two linear motifs in the intrinsically disordered linker domain (N3), a hydrophobic helix (219LALLLLDRLNQL230) and a disordered polar strand (243GQTVTKKSAAEAS255), that mutually engage to form a bipartite interaction, folding N3 around Ubl1. This results in substantial collapse in the dimensions of dimeric N, forming a highly compact molecular chaperone, that regulates binding to RNA, suggesting a key role of nsp3 in the association of N to the RTC. The identification of distinct linear motifs that mediate an important interaction between essential viral factors provides future targets for development of innovative strategies against COVID-19.

Intrinsically Disordered Tardigrade Proteins Self-Assemble into Fibrous Gels in Response to Environmental Stress

Tardigrades are remarkable for their ability to survive harsh stress conditions as diverse as extreme temperature and desiccation. The molecular mechanisms that confer this unusual resistance to physical stress remain unknown. Recently, tardigrade-unique intrinsically disordered proteins have been shown to play an essential role in tardigrade anhydrobiosis. Here, we characterize the conformational and physical behaviour of CAHS-8 from Hypsibius exemplaris. NMR spectroscopy reveals that the protein comprises an extended central helical domain flanked by disordered termini. Upon concentration, the protein is shown to successively form oligomers, long fibres, and finally gels constituted of fibres in a strongly temperature-dependent manner. The helical domain forms the core of the fibrillar structure, with the disordered termini remaining highly dynamic within the gel. Soluble proteins can be encapsulated within cavities in the gel, maintaining their functional form. The ability to reversibly form fibrous gels may be associated with the enhanced protective properties of these proteins.

1H, 13C and 15N Backbone chemical shift assignments of the n-terminal and central intrinsically disordered domains of SARS-CoV-2 nucleoprotein

The nucleoprotein (N) from SARS-CoV-2 is an essential cofactor of the viral replication transcription complex and as such represents an important target for viral inhibition. It has also been shown to colocalize to the transcriptase-replicase complex, where many copies of N decorate the viral genome, thereby protecting it from the host immune system. N has also been shown to phase separate upon interaction with viral RNA. N is a 419 amino acid multidomain protein, comprising two folded, RNA-binding and dimerization domains spanning residues 45-175 and 264-365 respectively. The remaining 164 amino acids are predicted to be intrinsically disordered, but there is currently no atomic resolution information describing their behaviour. Here we assign the backbone resonances of the first two intrinsically disordered domains (N1, spanning residues 1-44 and N3, spanning residues 176-263). Our assignment provides the basis for the identification of inhibitors and functional and interaction studies of this essential protein.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

1H, 13C and 15N backbone chemical shift assignments of SARS-CoV-2 nsp3a

The non-structural protein nsp3 from SARS-CoV-2 plays an essential role in the viral replication transcription complex. Nsp3a constitutes the N-terminal domain of nsp3, comprising a ubiquitin-like folded domain and a disordered acidic chain. This region of nsp3a has been linked to interactions with the viral nucleoprotein and the structure of double membrane vesicles. Here, we report the backbone resonance assignment of both domains of nsp3a. The study is carried out in the context of the international covid19-nmr consortium, which aims to characterize SARS-CoV-2 proteins and RNAs, providing for example NMR chemical shift assignments of the different viral components. Our assignment will provide the basis for the identification of inhibitors and further functional and interaction studies of this essential protein.

Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly

Many viruses are known to form cellular compartments, also called viral factories. Paramyxoviruses, including measles virus, colocalize their proteomic and genomic material in puncta in infected cells. We demonstrate that purified nucleoproteins (N) and phosphoproteins (P) of measles virus form liquid-like membraneless organelles upon mixing in vitro. We identify weak interactions involving intrinsically disordered domains of N and P that are implicated in this process, one of which is essential for phase separation. Fluorescence allows us to follow the modulation of the dynamics of N and P upon droplet formation, while NMR is used to investigate the thermodynamics of this process. RNA colocalizes to droplets, where it triggers assembly of N protomers into nucleocapsid-like particles that encapsidate the RNA. The rate of encapsidation within droplets is enhanced compared to the dilute phase, revealing one of the roles of liquid-liquid phase separation in measles virus replication.

P1752 Prognostic role of Multilayer Strain Speckle Tracking Echocardiography in patients with severe aortic stenosis treated with Transcatheter Aortic Valve Implantation

Background

Myocardial Strain evaluation helps to assess the efficacy of therapeutic interventions and to predict the prognosis and clinical outcomes. The aim of the present study was to assess whether Multilayer Global longitudinal Strain (GLS) can be useful in estimation of left ventricle (LV) function in patients with severe symptomatic aortic stenosis (AS) who have undergone transcatheter aortic valve implantation (TAVI).

Methods

35 patients with severe AS who successfully underwent TAVI, were enrolled in the study. GLS was measured from the endocardial layer (Endo-LS), epicardial layer (Epi-LS) and full thickness of myocardium before the procedure. Analysis included other parameters such as age, sex, LV volumes and ejection fraction (LVEF), type of prosthesis implanted, right ventricular (RV) dimension and function. Occurrence of cardiovascular (CV) events (rehospitalization for HF or CV death) were collected after 24 months follow-up.Results: CV events occurred in 7 patients (20%). Patients were divided in two groups accordingly with CV events occurrence. No differences in baseline, demographic, echocardiographic and procedural characteristics were found. Patients who developed CV events had a more impaired pre-procedural GLS (-10.2 ± 2.4% vs -12.6 ± 2.2%, p = 0.029), mostly due to his subendocardial layer (Endo-LS -10.8 ± 2 vs -13.9 ± 2, p = 0.003). Moreover, by ROC curve analysis, a cut-off value of -12.4% of endo LS was associated with CV events (sensitivity of 83% and specificity of 65 %, AUC 0.8, p = 0.024), with a log-rank p value assessed by survival analysis of 0.044.

Conclusion

Multilayer GLS analysis could provide additional information for prognosis stratification in patients with severe symptomatic AS before TAVI, above and beyond assessment of LVEF alone.

Parameter Event-group (7/35 pz= 20%) Non-event group (28/35 pz= 80%) p Age (y.o) 86 ± 4 80 ± 7 NS LVEDV (ml) 112 ± 34 94 ± 32 NS LVESV (ml) 51.2 ± 6 56.9 ± 6 NS LVEF(%) 55.7 ± 6 56.9 ± 6 NS AVA (cm2) 0.77 ± 0.2 0.73 ± 0.2 NS GLS (%) -10.2 ± 2.4 -12.6 ± 2.2 0.029 Endo-LS (%) -10.8 ± 2 -13.9 ± 2 0.003 Epi-LS (%) -10.2 ± 2 -11.9 ± 2 NS

Abstract P1752 Figure.

P1365 Different response of myocardial contractility by layer following acute pressure unloading after transcatheter aortic valve implantation

Background

Transcatheter aortic valve implantation (TAVI) is an effective therapeutic option for severe symptomatic aortic stenosis (AS) with intermediate/high surgical risk. Aim of this study was to examine the acute effect of TAVI in terms of pressure unloading, on left ventricular (LV) mechanics using multilayer global longitudinal strain (GLS) by 2D speckle-tracking echocardiography (ST-E).

Methods

A total of 44 patients (mean age 81.8 ± 2, 34% male) with severe symptomatic AS and preserved LV ejection fraction (LVEF) underwent 2D echocardiography at baseline and 5 ± 2 days after TAVI. GLS was measured from the endocardial layer (Endo-LS), epicardial layer (Epi-LS) and full thickness of myocardium before and after the procedure. Analysis included other parameters such as age, sex, LV volumes and ejection fraction (LVEF), type of prosthesis implanted, right ventricular (RV) dimension and function.

Results

By dividing patients in two groups accordingly with LV geometry assessed with regional wall thickness measurement (concentric vs eccentric hypertrophy), better values of Endo-LS were recorded at baseline, in patients with concentric hypertrophy (-12.9 ± 2 vs -11 ± 3, p = 0.048). After TAVI, a significant improvement in Endo-LS was observed, but only in patients with concentric hypertrophy (-12.9 ± 2 vs -14.2 ± 2, p = 0.003).

Conclusion

The improvement in LS was more prominent in the endocardium, which was evident even immediately after TAVI only in patients with concentric hypertrophy. Evaluation of multilayer strain may provide new insights into the positive effects of unloading in patients with AS and may be potentially useful to predict patients with better outcome after TAVI.

Parameter RWT > 0.42 31 pz (70%) RWT ≤ 0.42 13 pz (30%) p Male sex (n, %) 8 (25%) 7 (53%) NS Age (y.o) 81 ± 6 83 ± 7 NS CAD (n, %) 3 (9%) 8 (61%) NS LVEDV (ml) 97 ± 29 134 ± 14 0.002 LVESV (ml) 43 ± 15 72 ± 38 0.001 LVEF(%) 56.2 ± 6 50 ± 12 NS AVA (cm2) 0.8 ± 0.2 0.8 ± 0.3 NS GLS (%) -11.4 ± 3 -10.5 ± 3 NS Endo-LS (%) -12.9 ± 2 -11 ± 3 0.048 Epi-LS (%) -10.8 ± 4 -9.9 ± 3 NS

Abstract P1365 Figure.

A Unified Description of Intrinsically Disordered Protein Dynamics under Physiological Conditions Using NMR Spectroscopy

Intrinsically disordered proteins (IDPs) are flexible biomolecules whose essential functions are defined by their dynamic nature. Nuclear magnetic resonance (NMR) spectroscopy is ideally suited to the investigation of this behavior at atomic resolution. NMR relaxation is increasingly used to detect conformational dynamics in free and bound forms of IDPs under conditions approaching physiological, although a general framework providing a quantitative interpretation of these exquisitely sensitive probes as a function of experimental conditions is still lacking. Here, measuring an extensive set of relaxation rates sampling multiple-time-scale dynamics over a broad range of crowding conditions, we develop and test an integrated analytical description that accurately portrays the motion of IDPs as a function of the intrinsic properties of the crowded molecular environment. In particular we observe a strong dependence of both short-range and long-range motional time scales of the protein on the friction of the solvent. This tight coupling between the dynamic behavior of the IDP and its environment allows us to develop analytical expressions for protein motions and NMR relaxation properties that can be accurately applied over a vast range of experimental conditions. This unified dynamic description provides new insight into the physical behavior of IDPs, extending our ability to quantitatively investigate their conformational dynamics under complex environmental conditions, and accurately predicting relaxation rates reporting on motions on time scales up to tens of nanoseconds, both in vitro and in cellulo.

P6329123-Iodine Metaiodobenzylguanitidine imaging: a useful prognostic marker of cardiovascular death in heart failure patients

Background

According to guidelines, implantable cardioverter defibrillator (ICD) is recommended in prevention of sudden cardiac death (SCD) in heart failure (HF) patients (pts). Guidelines have several limitations because ICD indication is based mainly on left ventricular ejection fraction (LVEF). Recently, 123-iodine metaiodobenzylguanidine imaging (123-I MIBG) seems to identify, independently from LVEF, pts at high risk of SCD: heart/mediastinum (H/M) ratio<1.6 and summed score (SS)>26.

Purpose

The aim is to assess the role of 123-I MIBG to predict malignant ventricular arrhythmias (VA) in HF pts

Methods

We enrolled 208 pts, admitted to our hospital with diagnosis of HF and LVEF≤35%, NYHA class II and III, who underwent 123-I MIBG imaging. H/M ratio of 1.6 was used as a cut-off to identify high risk (G1) versus low risk pts (G2). All pts underwent ICD implantation. Follow-up was performed at 24 months.

Results

138 patients were included in G1 and 70 patients in G2. All baseline characteristics were similar in the two groups (table 1). At 24 months follow-up VA events were recorded greater in G1 compared to G2 (21% vs 10%, p=0.04).

Table 1 G1 G2 P value H/M ≤1.6 (N=138) H/M >1.6 (N=70) Age (years) 65±12 63±14 0.28 Male, N (%) 108 (78) 64 (91) 0.02 Diabetes mellitus type II, N (%) 54 (39) 14 (20) 0.01 Dyslipidemia, N (%) 58 (42) 30 (42) 0.64 LVEF (%) 30±5 31±4 0.14 Ischaemic CM, N (%) 85 (62) 30 (42) 0.012 Malignant VA, N (%) 30 (21) 7 (10) 0.04 SS 38±9 16±7 0.0001 H/M: heart mediastinum ratio; LVEF: left ventricular ejection fraction; CM: cardiomyopathy; VA: ventricular arrhythmias; SS: summed score.

Conclusion

Our results seem to confirm that 123-I MIBG uptake is associated with the occurrence of life-threatening VA in HF pts independently from LVEF. The use of 123-I MIBG could be a useful tool in the future to increase the specificity of the pts selection for ICD therapy.

The ESC ACCA EAPCI EORP acute coronary syndrome ST-elevation myocardial infarction registry

Aims 

The Acute Cardiac Care Association (ACCA)–European Association of Percutaneous Coronary Intervention (EAPCI) Registry on ST-elevation myocardial infarction (STEMI) of the EurObservational programme (EORP) of the European Society of Cardiology (ESC) registry aimed to determine the current state of the use of reperfusion therapy in ESC member and ESC affiliated countries and the adherence to ESC STEMI guidelines in patients with STEMI.

Methods and results 

Between 1 January 2015 and 31 March 2018, a total of 11 462 patients admitted with an initial diagnosis of STEMI according to the 2012 ESC STEMI guidelines were enrolled. Individual patient data were collected across 196 centres and 29 countries. Among the centres, there were 136 percutaneous coronary intervention centres and 91 with cardiac surgery on-site. The majority of centres (129/196) were part of a STEMI network. The main objective of this study was to describe the demographic, clinical, and angiographic characteristics of patients with STEMI. Other objectives include to assess management patterns and in particular the current use of reperfusion therapies and to evaluate how recommendations of most recent STEMI European guidelines regarding reperfusion therapies and adjunctive pharmacological and non-pharmacological treatments are adopted in clinical practice and how their application can impact on patients’ outcomes. Patients will be followed for 1 year after admission.

Conclusion 

The ESC ACCA-EAPCI EORP ACS STEMI registry is an international registry of care and outcomes of patients hospitalized with STEMI. It will provide insights into the contemporary patient profile, management patterns, and 1-year outcome of patients with STEMI.

Solvent-dependent segmental dynamics in intrinsically disordered proteins

Protein and water dynamics have a synergistic relationship, which is particularly important for intrinsically disordered proteins (IDPs), although the details of this coupling remain poorly understood. Here, we combine temperature-dependent molecular dynamics simulations using different water models with extensive nuclear magnetic resonance (NMR) relaxation to examine the importance of distinct modes of solvent and solute motion for the accurate reproduction of site-specific dynamics in IDPs. We find that water dynamics play a key role in motional processes internal to "segments" of IDPs, stretches of primary sequence that share dynamic properties and behave as discrete dynamic units. We identify a relationship between the time scales of intrasegment dynamics and the lifetime of hydrogen bonds in bulk water. Correct description of these motions is essential for accurate reproduction of protein relaxation. Our findings open important perspectives for understanding the role of hydration water on the behavior and function of IDPs in solution.

Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments

Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments. We describe the complementarity of different NMR parameters for quantifying the conformational propensities of IDPs in their isolated and phosphorylated states, and we discuss the challenges associated with obtaining structural models of dynamic protein-protein complexes involving IDPs. In addition, we review recent progress in understanding the conformational behavior of IDPs in cell-like environments such as in the presence of crowding agents, in membrane-less organelles and in the complex environment of the human cell.

Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity

Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline β2m. The destabilization of the outer strands of D76N β2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins.

The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R_1ρ, Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental approaches for investigating the conformational behaviour of intrinsically disordered proteins (IDPs). IDPs represent a significant fraction of all proteomes, and, despite their importance for understanding fundamental biological processes, the molecular basis of their activity still remains largely unknown. The functional mechanisms exploited by IDPs in their interactions with other biomolecules are defined by their intrinsic dynamic modes and associated timescales, justifying the considerable interest over recent years in the development of technologies adapted to measure and describe this behaviour. NMR spin relaxation delivers information-rich, site-specific data reporting on conformational fluctuations occurring throughout the molecule. Here we review recent progress in the use of ¹⁵N relaxation to identify local backbone dynamics and long-range chain-like motions in unfolded proteins.

Analytical Description of NMR Relaxation Highlights Correlated Dynamics in Intrinsically Disordered Proteins

The dynamic fluctuations of intrinsically disordered proteins (IDPs) define their function. Although experimental nuclear magnetic resonance (NMR) relaxation reveals the motional complexity of these highly flexible proteins, the absence of physical models describing IDP dynamics hinders their mechanistic interpretation. Combining molecular dynamics simulation and NMR, we introduce a framework in which distinct motions are attributed to local libration, backbone dihedral angle dynamics and longer-range tumbling of one or more peptide planes. This model provides unique insight into segmental organization of dynamics in IDPs and allows us to investigate the presence and extent of the correlated motions that are essential for function.

Dynamic Descriptions of Highly Flexible Molecules from NMR Dipolar Couplings: Physical Basis and Limitations

Biomolecules that control physiological function by changing their conformation play key roles in biology and remain poorly characterized. NMR dipolar couplings (DCs) depend intrinsically on both molecular shape and structural fluctuations, thereby providing the enticing prospect of tracking these conformational changes at atomic detail. Although this dual dependence has until now severely complicated analysis of DCs from highly dynamic systems, general approaches have recently been proposed that simplify interpretation of experimental DCs, by entirely eliminating molecular alignment from the analysis. Using simple and intuitive simulation of target ensembles, we investigate the impact of such approaches on the resulting descriptions of the conformational energy landscape. We find that ensemble descriptions of highly flexible systems derived from DCs without explicit consideration of the alignment properties of the constituent conformations can be compromised and inaccurate, despite exhibiting high correlation with experimental measurement.

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation

Intrinsically disordered proteins (IDPs) access highly diverse ensembles of conformations in their functional states. Although this conformational plasticity is essential to their function, little is known about the dynamics underlying interconversion between accessible states. Nuclear magnetic resonance (NMR) relaxation rates contain a wealth of information about the time scales and amplitudes of motion in IDPs, but the highly dynamic nature of IDPs complicates their interpretation. We present a novel framework in which a series of molecular dynamics (MD) simulations are used in combination with experimental (15)N relaxation measurements to characterize the ensemble of dynamic processes contributing to the observed rates. By accounting for the distinct dynamic averaging present in the different conformational states sampled by the equilibrium ensemble, we are able to accurately describe both dynamic time scales and local and global conformational sampling. The method is robust, systematically improving agreement with independent experimental relaxation data, irrespective of the actively targeted rates, and suggesting interdependence of motions occurring on time scales varying over 3 orders of magnitude.

Challenges in preparing, preserving and detecting para-water in bulk: overcoming proton exchange and other hurdles

Para-water is an analogue of para-hydrogen, where the two proton spins are in a quantum state that is antisymmetric under permutation, also known as singlet state. The populations of the nuclear spin states in para-water are believed to have long lifetimes just like other Long-Lived States (LLSs). This hypothesis can be verified by measuring the relaxation of an excess or a deficiency of para-water, also known as a "Triplet-Singlet Imbalance" (TSI), i.e., a difference between the average population of the three triplet states T (that are symmetric under permutation) and the population of the singlet state S. In analogy with our recent findings on ethanol and fumarate, we propose to adapt the procedure for Dissolution Dynamic Nuclear Polarization (D-DNP) to prepare such a TSI in frozen water at very low temperatures in the vicinity of 1.2 K. After rapid heating and dissolution using an aprotic solvent, the TSI should be largely preserved. To assess this hypothesis, we studied the lifetime of water as a molecular entity when diluted in various solvents. In neat liquid H2O, proton exchange rates have been characterized by spin-echo experiments on oxygen-17 in natural abundance, with and without proton decoupling. One-dimensional exchange spectroscopy (EXSY) has been used to study proton exchange rates in H2O, HDO and D2O mixtures diluted in various aprotic solvents. In the case of 50 mM H2O in dioxane-d8, the proton exchange lifetime is about 20 s. After dissolving, one can observe this TSI by monitoring intensities in oxygen-17 spectra of H2O (if necessary using isotopically enriched samples) where the AX2 system comprising a "spy" oxygen A and two protons X2 gives rise to binomial multiplets only if the TSI vanishes. Alternatively, fast chemical addition to a suitable substrate (such as an activated aldehyde or ketone) can provide AX2 systems where a carbon-13 acts as a spy nucleus. Proton signals that relax to equilibrium with two distinct time constants can be considered as a hallmark of a TSI. We optimized several experimental procedures designed to preserve and reveal dilute para-water in bulk.

Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation

Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach.

The Role of Dynamics and Allostery in the Inhibition of the eIF4E/eIF4G Translation Initiation Factor Complex

Lack of regulation of the interaction between the eIF4E/eIF4G subunits of the translation initiation factor complex eIF4F is a hallmark of cancer. The inhibitor 4EGI-1 binds to eIF4E, thereby preventing association with eIF4G through an allosteric mechanism. NMR spectroscopy and MD simulations were used to obtain a mechanistic description of the role of correlated dynamics in this allosteric regulation. We show that binding of 4EGI-1 perturbs native correlated motions and increases correlated fluctuations in part of the eIF4G binding site.

Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation

The dynamic modes and time scales sampled by intrinsically disordered proteins (IDPs) define their function. Nuclear magnetic resonance (NMR) spin relaxation is probably the most powerful tool for investigating these motions delivering site-specific descriptions of conformational fluctuations from throughout the molecule. Despite the abundance of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rates remains poorly understood. Here we measure an extensive range of auto- and cross-correlated spin relaxation rates at multiple magnetic field strengths on the C-terminal domain of the nucleoprotein of Sendai virus, over a large range of temperatures (268-298 K), and combine these data to describe the dynamic behavior of this archetypal IDP. An Arrhenius-type relationship is used to simultaneously analyze up to 61 relaxation rates per amino acid over the entire temperature range, allowing the measurement of local activation energies along the chain, and the assignment of physically distinct dynamic modes. Fast (τ ≤ 50 ps) components report on librational motions, a dominant mode occurs on time scales around 1 ns, apparently reporting on backbone sampling within Ramachandran substates, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. Extending the study to three protein constructs of different lengths (59, 81, and 124 amino acids) substantiates the assignment of these contributions. The analysis is shown to be remarkably robust, accurately predicting a broad range of relaxation data measured at different magnetic field strengths and temperatures. The ability to delineate intrinsic modes and time scales from NMR spin relaxation will improve our understanding of the behavior and function of IDPs, adding a new and essential dimension to the description of this biologically important and ubiquitous class of proteins.

Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins

Adiabatically swept pulses were originally designed for the purpose of broadband spin inversion. Later, unexpected advantages of their utilization were also found in other applications, such as refocusing to excite spin echoes, studies of chemical exchange or fragment-based drug design. Here, we present new experiments to characterize fast (ps-ns) protein dynamics, which benefit from little-known properties of adiabatic pulses. We developed a strategy for measuring cross-correlated cross-relaxation (CCCR) rates during adiabatic pulses. This experiment provides a linear combination of longitudinal and transverse CCCR rates, which is offset-independent across a typical amide (15)N spectrum. The pulse sequence can be recast to provide accurate transverse CCCR rates weighted by the populations of exchanging states. Sensitivity can be improved in systems in slow exchange. Finally, the experiments can be easily modified to yield residue-specific correlation times. The average correlation time of motions can be determined with a single experiment while at least two different experiments had to be recorded until now.

Theoretical tools for the design of NMR relaxation dispersion pulse sequences

Recent decades have witnessed tremendous progress in the development of new experimental methods for studying biomolecules, particularly in the field of NMR relaxation dispersion. Here we review the theoretical frameworks that provided the insights necessary for such progress. The effect of radio-frequency manipulations on spin systems is discussed using Average Hamiltonian Theory (AHT), Average Liouvillian Theory (ALT), and Bloch-Wangsness-Redfield (BWR) relaxation theory. We illustrate these concepts using the case of Heteronuclear Double Resonance (HDR) methods.

Drug screening boosted by hyperpolarized long-lived states in NMR

Transverse and longitudinal relaxation times (T_1ρ and T₁) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long-lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T₁(¹H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D-DNP). Hyperpolarized weak “spy ligands” can be displaced by high-affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput.

Solid-state carbon-13 NMR and computational characterization of the N719 ruthenium sensitizer adsorbed on TiO₂ nanoparticles

The ruthenium-containing sensitizing dye N719 grafted on TiO2 nanoparticles was investigated by solid-state NMR. The carbon resonances are assigned by means of (13)C cross-polarized dipolar dephasing experiments. DFT calculations of the carbon magnetic shielding tensors accurately describe the changes in chemical shifts observed upon grafting onto a titania surface via one or two carboxylic functions in the plane defined by the two isothiocyanate groups.

[Anesthesia in spontaneous ventilation for difficult intubation]

Difficult intubation in children is rare and often predictable during anesthesia consultation. This allows to establish a strategy to provide fiberoptic guided tracheal intubation with spontaneous ventilation in function of age and children pathology. A good knowledge of physiologic and anatomic children particularities, of fiberoptic technique and the respect for some principles lead to ensure the security of this procedure. First principle is to use only one anesthetic inhaled or intravenous agent in order to limit an important decrease of ventilation. The anesthetic technique recommended for pediatric fiberoptic guided intubation is inhaled anesthesia with sevoflurane. But it is possible to use an intravenous agent, like propofol, with a continuous infusion (bolus of 0.1 to 0.3 mg/kg then 0.1-0.3mg/kg per hour for maintenance) or with target controlled infusion (Schnider model, initial concentration 2.5 μg/mL, then increase by 0.5 μg/mL steps) particularly in children older than 5 years with an anesthetic depth control. Whatever the agent, the dose must to be titrated to maintain spontaneous ventilation. Second principle is to combine an airway local anesthesia with general anesthesia to limit airway reactivity. First, a nose topical anesthesia is administered with lidocaine plus naphazoline in children older than 2 years. Then, a laryngeal topical anesthesia is realized with lidocaine 1% (1-2 mL, 2mg/kg) through operating channel of fiberoptic bronchoscope. Finally, third principle is to ensure patient oxygenation with several techniques like use of endoscopic facial mask or nasopharyngeal tube. The use of laryngeal mask is a rescue technique in case of spontaneous ventilation lost. In conclusion, each institution has to establish an algorithm with his own knowledge, constantly feasible and regularly taught.

Dynamic Nuclear Polarization and other magnetic ideas at EPFL

Although nuclear magnetic resonance (NMR) can provide a wealth of information, it often suffers from a lack of sensitivity. Dynamic Nuclear Polarization (DNP) provides a way to increase the polarization and hence the signal intensities in NMR spectra by transferring the favourable electron spin polarization of paramagnetic centres to the surrounding nuclear spins through appropriate microwave irradiation. In our group at EPFL, two complementary DNP techniques are under investigation: the combination of DNP with magic angle spinning at temperatures near 100 K ('MAS-DNP'), and the combination of DNP at 1.2 K with rapid heating followed by the transfer of the sample to a high-resolution magnet ('dissolution DNP'). Recent applications of MAS-DNP to surfaces, as well as new developments of magnetization transfer of (1)H to (13)C at 1.2 K prior to dissolution will illustrate the work performed in our group. A second part of the paper will give an overview of some 'non-enhanced' activities of our laboratory in liquid- and solid-state NMR.

Boosting the sensitivity of ligand-protein screening by NMR of long-lived states

A new NMR method for the study of ligand-protein interactions exploits the unusual lifetimes of long-lived states (LLSs). The new method provides better contrast between bound and free ligands and requires a protein-ligand ratio ca. 25 times lower than for established T(1ρ) methods, thus saving on costly proteins. The new LLS method was applied to the screening of inhibitors of urokinase-type plasminogen activator (uPA), which is a prototypical target of cancer research. With only 10 μM protein, a dissociation constant (K(D)) of 180 ± 20 nM was determined for the strong ligand (inhibitor) UK-18, which can be compared with K(D) = 157 ± 39 nM determined by the established surface plasmon resonance method.