Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals

NMR tools to detect protein allostery

Allostery is a fundamental mechanism of cellular homeostasis by intra-protein communication between distinct functional sites. It is an internal process of proteins to steer interactions not only with each other but also with other biomolecules such as ligands, lipids, and nucleic acids. In addition, allosteric regulation is particularly important in enzymatic activities. A major challenge in structural and molecular biology today is unraveling allosteric sites in proteins, to elucidate the detailed mechanism of allostery and the development of allosteric drugs. Here we summarize the recently developed tools and approaches which enable the elucidation of regulatory hotspots and correlated motion in biomolecules, focusing primarily on solution-state nuclear magnetic resonance spectroscopy (NMR). These tools open an avenue towards a rational understanding of the mechanism of allostery and provide essential information for the design of allosteric drugs.

Atomic resolution protein allostery from the multi-state structure of a PDZ domain

Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally and dynamically correlated protein sites at atomic resolution. This is demonstrated in the present work for the well-studied PDZ2 domain of protein human tyrosine phosphatase 1E for which protein allostery had been predicted. Two-state protein structures were calculated for both the free form and in complex with the RA-GEF2 peptide using the exact nuclear Overhauser effect (eNOE) method. In the apo protein, an allosteric conformational selection step comprising almost 60% of the domain was detected with an "open" ligand welcoming state and a "closed" state that obstructs the binding site by changing the distance between the β-sheet 2, α-helix 2, and sidechains of residues Lys38 and Lys72. The observed induced fit-type apo-holo structural rearrangements are in line with the previously published evolution-based analysis covering ~25% of the domain with only a partial overlap with the protein allostery of the open form. These presented structural studies highlight the presence of a dedicated highly optimized and complex dynamic interplay of the PDZ2 domain owed by the structure-dynamics landscape.

Advances in the exact nuclear Overhauser effect 2018-2022

The introduction of the exact nuclear Overhauser enhancement (eNOE) methodology to solution-state nuclear magnetic resonance (NMR) spectroscopy results in tighter distance restraints from NOEs than in convention analysis. These improved restraints allow for higher resolution in structure calculation and even the disentanglement of different conformations of macromolecules. While initial work primarily focused on technical development of the eNOE, structural studies aimed at the elucidation of spatial sampling in proteins and nucleic acids were published in parallel prior to 2018. The period of 2018-2022 saw a continued series of technical innovation, but also major applications addressing biological questions. Here, we review both aspects, covering topics from the implementation of non-uniform sampling of NOESY buildups, novel pulse sequences, adaption of the eNOE to solid-state NMR, advances in eNOE data analysis, and innovations in structural ensemble calculation, to applications to protein, RNA, and DNA structure elucidation.

On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins

Residual dipolar couplings (RDCs) are powerful nuclear magnetic resonance (NMR) probes for the structure calculation of biomacromolecules. Typically, an alignment tensor that defines the orientation of the entire molecule relative to the magnetic field is determined either before refinement of individual bond vectors or simultaneously with this refinement. For single-domain proteins this approach works well since all bond vectors can be described within the same coordinate frame, which is given by the alignment tensor. However, novel approaches are sought after for systems where no universal alignment tensor can be used. Here, we present an approach that can be applied to two-domain proteins that enables the calculation of multiple states within each domain as well as with respect to the relative positions of the two domains.

PDBcor: An automated correlation extraction calculator for multi-state protein structures

Allostery and correlated motion are key elements linking protein dynamics with the mechanisms of action of proteins. Here, we present PDBCor, an automated and unbiased method for the detection and analysis of correlated motions from experimental multi-state protein structures. It uses torsion angle and distance statistics and does not require any structure superposition. Clustering of protein conformers allows us to extract correlations in the form of mutual information based on information theory. With PDBcor, we elucidated correlated motion in the WW domain of PIN1, the protein GB3, and the enzyme cyclophilin, in line with reported findings. Correlations extracted with PDBcor can be utilized in subsequent assays including nuclear magnetic resonance (NMR) multi-state structure optimization and validation. As a guide for the interpretation of PDBcor results, we provide a series of protein structure ensembles that exhibit different levels of correlation, including non-correlated, locally correlated, and globally correlated ensembles.

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance

Proteins composed of multiple domains allow for structural heterogeneity and interdomain dynamics that may be vital for function. Intradomain structures and dynamics can influence interdomain conformations and vice versa. However, no established structure determination method is currently available that can probe the coupling of these motions. The protein Pin1 contains separate regulatory and catalytic domains that sample "extended" and "compact" states, and ligand binding changes this equilibrium. Ligand binding and interdomain distance have been shown to impact the activity of Pin1, suggesting interdomain allostery. In order to characterize the conformational equilibrium of Pin1, we describe a novel method to model the coupling between intra- and interdomain dynamics at atomic resolution using multistate ensembles. The method uses time-averaged nuclear magnetic resonance (NMR) restraints and double electron-electron resonance (DEER) data that resolve distance distributions. While the intradomain calculation is primarily driven by exact nuclear Overhauser enhancements (eNOEs), J couplings, and residual dipolar couplings (RDCs), the relative domain distribution is driven by paramagnetic relaxation enhancement (PREs), RDCs, interdomain NOEs, and DEER. Our data support a 70:30 population of the compact and extended states in apo Pin1. A multistate ensemble describes these conformations simultaneously, with distinct conformational differences located in the interdomain interface stabilizing the compact or extended states. We also describe correlated conformations between the catalytic site and interdomain interface that may explain allostery driven by interdomain contact.

Protein Allostery at Atomic Resolution

Protein allostery is a phenomenon involving the long range coupling between two distal sites in a protein. In order to elucidate allostery at atomic resoluion on the ligand-binding WW domain of the enzyme Pin1, multistate structures were calculated from exact nuclear Overhauser effect (eNOE). In its free form, the protein undergoes a microsecond exchange between two states, one of which is predisposed to interact with its parent catalytic domain. In presence of the positive allosteric ligand, the equilibrium between the two states is shifted towards domain-domain interaction, suggesting a population shift model. In contrast, the allostery-suppressing ligand decouples the side-chain arrangement at the inter-domain interface thereby reducing the inter-domain interaction. As such, this mechanism is an example of dynamic allostery. The presented distinct modes of action highlight the power of the interplay between dynamics and function in the biological activity of proteins.

Reducing the measurement time of exact NOEs by non-uniform sampling

We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10 days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4 kDa protein human Pin1, the 4.1 kDa WW domain of Pin1 (both in 3D), and a 4.6 kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.

Protein Motional Details Revealed by Complementary Structural Biology Techniques

Proteins depend on defined molecular plasticity for their functionality. How to comprehensively capture dynamics correctly is of ubiquitous biological importance. Approaches commonly used to probe protein dynamics include model-free elucidation of site-specific motion by NMR relaxation, molecular dynamics (MD)-based approaches, and capturing the substates within a dynamic ensemble by recent eNOE-based multiple-structure approaches. Even though MD is sometimes combined with ensemble-averaged NMR restraints, these approaches have largely been developed and used individually. Owing to the different underlying concepts and practical requirements, it has remained unclear how they compare, and how they cross-validate and complement each other. Here, we extract and compare the differential information contents of MD simulations, NMR relaxation measurements, and eNOE-based multi-state structures for the SH3 domain of chicken α-spectrin. The data show that a validated, consistent, and detailed picture is feasible both for timescales and actual conformational states sampled in the dynamic ensemble. This includes the biologically important side-chain plasticity, for which experimentally cross-validated assessment is a significant challenge.

Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA

Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.

High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints

RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.

NOE-Derived Methyl Distances from a 360 kDa Proteasome Complex

Nuclear magnetic resonance spectroscopy is the prime tool to probe structure and dynamics of biomolecules at atomic resolution. A serious challenge for that method is the size limit imposed on molecules to be studied. Standard studies are typically restricted to ca. 30-40 kDa. More recent developments lead to spin relaxation measurements in methyl groups in single proteins or protein complexes as large as a mega-Dalton, which directly allow the extraction of angular information or experiments with paramagnetic samples. However, these probes are all of indirect nature in contrast to the most intuitive and easy-to-interpret structural/dynamics restraint, the internuclear distance, which can be measured by nuclear Overhauser enhancement (NOE). Herein, we demonstrate time-averaged distance measurements on the 360 kDa half proteasome from Thermoplasma acidophilium. The approach is based on exact quantification of the NOE (eNOE). Our findings open up an avenue for such measurements on very large molecules. These restraints will help in a detailed determination of conformational changes upon perturbation such as ligand binding.

eNORA2 Exact NOE Analysis Program

We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from an exact interpretation of NOESY buildup intensities (eNOEs). This enabled us to calculate multistate structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious and required a deep understanding of the underlying spin dynamics. Here, we present a MatLab package that integrates all data processing steps required to convert intensities of assigned peaks in NOESY series into upper and lower distance limits for structure calculation. Those steps include organization of the data in object format, extraction of autorelaxation and cross-relaxation rate constants by fitting of diagonal peak decays and cross peak buildups, validation of the data, correction for spin diffusion, graphical display of the results, and generation of distance limits in CYANA compatible format. The analysis may be carried out using a full relaxation matrix or a simplified "divide and conquer" approach that allows for partial deuteration of protons. As the program does not require expertise beyond that of standard resonance assignment/structure calculation, it is suitable for experts and nonexperts alike.

The Exact Nuclear Overhauser Enhancement: Recent Advances

Although often depicted as rigid structures, proteins are highly dynamic systems, whose motions are essential to their functions. Despite this, it is difficult to investigate protein dynamics due to the rapid timescale at which they sample their conformational space, leading most NMR-determined structures to represent only an averaged snapshot of the dynamic picture. While NMR relaxation measurements can help to determine local dynamics, it is difficult to detect translational or concerted motion, and only recently have significant advances been made to make it possible to acquire a more holistic representation of the dynamics and structural landscapes of proteins. Here, we briefly revisit our most recent progress in the theory and use of exact nuclear Overhauser enhancements (eNOEs) for the calculation of structural ensembles that describe their conformational space. New developments are primarily targeted at increasing the number and improving the quality of extracted eNOE distance restraints, such that the multi-state structure calculation can be applied to proteins of higher molecular weights. We then review the implications of the exact NOE to the protein dynamics and function of cyclophilin A and the WW domain of Pin1, and finally discuss our current research and future directions.

PDB2CD visualises dynamics within protein structures

Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

The Exact NOE as an Alternative in Ensemble Structure Determination

The structure-function paradigm is increasingly replaced by the structure-dynamics-function paradigm. All protein activity is steered by the interplay between enthalpy and entropy. Conformational dynamics serves as a proxy of conformational entropy. Therefore, it is essential to study not only the average conformation but also the spatial sampling of a protein on all timescales. To this purpose, we have established a protocol for determining multiple-state ensembles of proteins based on exact nuclear Overhauser effects (eNOEs). We have recently extended our previously reported eNOE data set for the protein GB3 by a very large set of backbone and side-chain residual dipolar couplings and three-bond J couplings. Here, we demonstrate that at least four structural states are required to represent the complete data set by dissecting the contributions to the CYANA target function, which quantifies restraint violations in structure calculation. We present a four-state ensemble of GB3, which largely preserves the characteristics obtained from eNOEs only. Due to the abundance of the input data, the ensemble and χ(1) angles in particular are well suited for cross-validation of the input data and comparison to x-ray structures. Principal component analysis is used to automatically identify and validate relevant states of the ensembles. Overall, our findings suggest that eNOEs are a valuable alternative to traditional NMR probes in spatial elucidation of proteins.