Cooperativity in protein-folding kinetics

Bringing the heat: Thermostable analogs of Bst polymerase allow high-temperature LAMP

BACKGROUND

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that gained prominence during the early months of the COVID-19 pandemic due to its simplicity, sensitivity and robustness. However, this technique is susceptible to non-specific amplifications, raising concerns about false-positive results and reduced diagnostic accuracy. A primary contributor to false-positive testing is primer dimerization, which can theoretically be mitigated by performing reactions at higher temperatures. Unfortunately, the strand-displacing DNA polymerases typically used in LAMP, such as Bst, exhibit reduced efficiency at elevated temperatures. To address this limitation, we hypothesised that naturally occurring thermophilic analogs of Bst may be capable of supporting LAMP at higher temperatures, thereby improving reaction specificity.

METHODS

Bioinformatics and recombinant enzyme production allowed the identification and synthesis of several Bst analogs. These were tested in real-time LAMP assays to detect diverse targets, in a wide range of reaction temperatures (63°C-75°C) and in the presence of typical qPCR inhibitors.

RESULTS

Three polymerases-Bst_7, Bst_8 and Bst_15-demonstrated exceptional activity and robust stability at higher temperature conditions (up to 72.5°C), while displaying considerable resistance to common qPCR inhibitors.

CONCLUSIONS

The identified thermophilic Bst analogs represent a potential solution for the mitigation of non-specific amplification in LAMP, further boosting the application of this technique in molecular diagnostic settings.

Beta Sandwich-Like Folds: Sequences, Contacts, Classification of Invariant Substructures and Beta Sandwich Protein Grammar

This chapter addresses the following fundamental question: Do sequences of protein domains with sandwich architecture have common sequence characteristics even though they belong to different superfamilies and folds? The analysis was carried out in two stages: (1) determination of domain substructures shared by all sandwich proteins and (2) detection of common sequence characteristics within the substructures. Analysis of supersecondary structures in domains of proteins revealed two types of four-strand substructures that are common to sandwich proteins. At least one of these common substructures was found in proteins of 42 sandwich-like folds (per structural classification in the CATH database). A comparison of sequence fragments and residue-residue contacts constituting common substructures revealed specific distributions of hydrophobic residues in these chains. The shared sequences and structural characteristics can be conceptualized as the "grammatical rules of beta protein linguistics." Understanding the structural and sequence commonalities of sandwich proteins may prove useful for rational protein design.

Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain

Engrailed homeodomain (EngHD), a highly charged transcription factor regulating over 200 genes, is a fast-folding protein. Recent studies have shown that the abundant charged residues in EngHD not only facilitate protein-DNA interactions but also influence the conformational disorder of its native structure. However, the mechanisms by which electrostatic interactions modulate the folding of EngHD remain unclear. Here, we employ a coarse-grained structure-based model that incorporates the salt-dependent Debye-Hückel model to investigate the (un)folding behavior of EngHD under various salt concentrations. Our findings demonstrate that increasing salt concentrations enhance both folding stability and cooperativity, while the folding barrier height remains relatively constant due to the distinct electrostatic effects on individual residues. By modulating the energetic balance between local and nonlocal interactions, we shift the folding of EngHD from a downhill process to a two-state process. Notably, we observe a nonmonotonic relationship between the strength of local interactions and residue-level coupling degree during (un)folding, likely attributed to the repulsive electrostatic interactions present in the native structure of EngHD. Additionally, we identify a critical turning point in the dependence of folding cooperativity on salt concentration, classified by the energetic balance of local and nonlocal interactions. Our results provide valuable insights into how electrostatic interactions influence the folding of EngHD, contributing to the theoretical framework for engineering highly charged proteins.

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

The folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1

De novo mutations in the synaptic GTPase activating protein (SynGAP) are associated with neurological disorders like intellectual disability, epilepsy, and autism. SynGAP is also implicated in Alzheimer's disease and cancer. Although pathogenic variants are highly penetrant in neurodevelopmental conditions, a substantial number of them are caused by missense mutations that are difficult to diagnose. Hence, in silico mutagenesis was performed for probing the missense effects within the N-terminal region of SynGAP structure. Through extensive molecular dynamics simulations, encompassing three 150-ns replicates for 211 variants, the impact of missense mutations on the protein fold was assessed. The effect of the mutations on the folding stability was also quantitatively assessed using free energy calculations. The mutations were categorized as potentially pathogenic or benign based on their structural impacts. Finally, the study introduces wild-type-SynGAP in complex with RasGTPase at the inner membrane, while considering the potential effects of mutations on these key interactions. This study provides structural perspective to the clinical assessment of SynGAP missense variants and lays the foundation for future structure-based drug discovery.

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins

Conformational properties of intrinsically disordered proteins (IDPs) are governed by a sequence-ensemble relationship. To differentiate the impact of sequence-local versus sequence-nonlocal features of an IDP's charge pattern on its conformational dimensions and its phase-separation propensity, the charge "blockiness" κ and the nonlocality-weighted sequence charge decoration (SCD) parameters are compared for their correlations with isolated-chain radii of gyration (Rgs) and upper critical solution temperatures (UCSTs) of polyampholytes modeled by random phase approximation, field-theoretic simulation, and coarse-grained molecular dynamics. SCD is superior to κ in predicting Rg because SCD accounts for effects of contact order, i.e., nonlocality, on dimensions of isolated chains. In contrast, κ and SCD are comparably good, though nonideal, predictors of UCST because frequencies of interchain contacts in the multiple-chain condensed phase are less sensitive to sequence positions than frequencies of intrachain contacts of an isolated chain, as reflected by κ correlating better with condensed-phase interaction energy than SCD.

Effects of Macromolecular Cosolutes on the Kinetics of Huntingtin Aggregation Monitored by NMR Spectroscopy

The effects of two macromolecular cosolutes, specifically the polysaccharide dextran-20 and the protein lysozyme, on the aggregation kinetics of a pathogenic huntingtin exon-1 protein (hhtex1) with a 35 polyglutamine repeat, httex1Q35, are described. A unified kinetic model that establishes a direct connection between reversible tetramerization occurring on the microsecond time scale and irreversible fibril formation on a time scale of hours/days forms the basis for quantitative analysis of httex1Q35 aggregation, monitored by measuring cross-peak intensities in a series of 2D 1H-15N NMR correlation spectra acquired during the course of aggregation. The primary effects of the two cosolutes are associated with shifts in the prenucleation tetramerization equilibrium resulting in substantial changes in concentration of "preformed" httex1Q35 tetramers. Similar effects of the two cosolutes on the tetramerization equilibrium observed for a shorter, nonaggregating huntingtin variant with a 7-glutamine repeat, httex1Q7, lend confidence to the conclusions drawn from the fits to the httex1Q35 aggregation kinetics.

Nucleation of Huntingtin Aggregation Proceeds via Conformational Conversion of Pre-Formed, Sparsely-Populated Tetramers

Pathogenic huntingtin exon-1 protein (httex1), characterized by an expanded polyglutamine tract located between the N-terminal amphiphilic region and a C-terminal polyproline-rich domain, forms fibrils that accumulate in neuronal inclusion bodies, and is associated with a fatal, autosomal dominant neurodegenerative condition known as Huntington's disease. Here a complete kinetic model is described for aggregation/fibril formation of a httex1 construct with a 35-residue polyglutamine repeat, httex1Q35. Using exchange NMR spectroscopy, it is previously shown that the reversible formation of a sparsely-populated tetramer of the N-terminal amphiphilic domain of httex1Q35, comprising a D2 symmetric four-helix bundle, occurs on the microsecond time-scale and is a prerequisite for subsequent nucleation and fibril formation on a time scale that is many orders of magnitude slower (hours). Here a unified kinetic model of httex1Q35 aggregation is developed in which fast, reversible tetramerization is directly linked to slow irreversible fibril formation via conversion of pre-equilibrated tetrameric species to "active", chain elongation-capable nuclei by conformational re-arrangement with a finite, monomer-independent rate. The unified model permits global quantitative analysis of reversible tetramerization and irreversible fibril formation from a time series of 1H-15N correlation spectra recorded during the course of httex1Q35 aggregation.

On the role of native contact cooperativity in protein folding

The consistency of energy landscape theory predictions with available experimental data, as well as direct evidence from molecular simulations, have shown that protein folding mechanisms are largely determined by the contacts present in the native structure. As expected, native contacts are generally energetically favorable. However, there are usually at least as many energetically favorable nonnative pairs owing to the greater number of possible nonnative interactions. This apparent frustration must therefore be reduced by the greater cooperativity of native interactions. In this work, we analyze the statistics of contacts in the unbiased all-atom folding trajectories obtained by Shaw and coworkers, focusing on the unfolded state. By computing mutual cooperativities between contacts formed in the unfolded state, we show that native contacts form the most cooperative pairs, while cooperativities among nonnative or between native and nonnative contacts are typically much less favorable or even anticooperative. Furthermore, we show that the largest network of cooperative interactions observed in the unfolded state consists mainly of native contacts, suggesting that this set of mutually reinforcing interactions has evolved to stabilize the native state.

Function of the Conserved Non-Functional Residues in Apomyoglobin - to Determine and to Preserve Correct Topology of the Protein

In this paper the answer to O. B. Ptitsyn's question "What is the role of conserved non-functional residues in apomyoglobin" is presented, which is based on the research results of three laboratories. The role of conserved non-functional apomyoglobin residues in formation of native topology in the molten globule state of this protein is revealed. This fact allows suggesting that the conserved non-functional residues in this protein are indispensable for fixation and maintaining main elements of the correct topology of its secondary structure in the intermediate state. The correct topology is a native element in the intermediate state of the protein.

The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water

Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or "beacons"). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water.

Predicting non-equilibrium folding behavior of polymer chains using the steepest-entropy-ascent quantum thermodynamic framework

The steepest-entropy-ascent quantum thermodynamic (SEAQT) framework is used to explore the influence of heating and cooling on polymer chain folding kinetics. The framework predicts how a chain moves from an initial non-equilibrium state to stable equilibrium along a unique thermodynamic path. The thermodynamic state is expressed by occupation probabilities corresponding to the levels of a discrete energy landscape. The landscape is generated using the Replica Exchange Wang-Landau method applied to a polymer chain represented by a sequence of hydrophobic and polar monomers with a simple hydrophobic-polar amino acid model. The chain conformation evolves as energy shifts among the levels of the energy landscape according to the principle of steepest entropy ascent. This principle is implemented via the SEAQT equation of motion. The SEAQT framework has the benefit of providing insight into structural properties under non-equilibrium conditions. Chain conformations during heating and cooling change continuously without sharp transitions in morphology. The changes are more drastic along non-equilibrium paths than along quasi-equilibrium paths. The SEAQT-predicted kinetics are fitted to rates associated with the experimental intensity profiles of cytochrome c protein folding with Rouse dynamics.

Hereditary Vitamin D-Resistant Rickets (HVDRR) associated SNP variants of vitamin D receptor exhibit malfunctioning at multiple levels

Vitamin D receptor (VDR) is a member of the nuclear receptor superfamily. It is a primary regulator of calcium and phosphate homeostasis required for skeleton and bone mineralization. Vitamin D in active form 1α,25 dihydroxyvitamin-D3 mediates its cellular functions by binding to VDR. Active VDR forms heterodimers with partner RXR (retinoid X receptor) to execute its physiological actions. HVDRR (Hereditary Vitamin D-Resistant Rickets) is a rare genetic disorder that occurs because of generalized resistance to the 1α,25(OH)₂D3. HVDRR is caused by the polymorphic variations in VDR gene leading to defective intestinal calcium absorption and mineralization of newly forming bones. Using point and deletion SNPs of VDR we have studied several HVDRR-associated SNP variants for their subcellular dynamics, transcriptional functions, 'genome bookmarking', heterodimeric interactions with RXR, and receptor stability. We previously reported that VDR is a 'mitotic bookmarking factor' that remains constitutively associated with the mitotic chromatin to inherit 'transcriptional memory', however the mechanistic details remained unclear. We document that 'genome bookmarking' property by VDR is critically impaired by naturally occurring HVDRR-associated point and deletion variants found in patients. Furthermore, these HVDRR-associated SNP variants of VDR were found to be compromised in transcriptional function, nuclear translocation, protein stability and intermolecular interactions with its heterodimeric partner RXR. Intriguingly, majority of these disease-allied functional defects failed to be rescued by RXR. Our findings suggest that the HVDRR-associated SNP variations influence the normal functioning of the receptor, and this derived understanding may help in the management of disease with precisely designed small molecule modulators.

Some useful ideas for multistate protein design: Effect of amino acid substitutions on the multistate proteins stability and the rate of protein structure formation

The design of new protein variants is usually confined to slightly “fixing” an already existing protein, adapting it to certain conditions or to a new substrate. This is relatively easy to do if the fragment of the protein to be affected, such as the active site of the protein, is known. But what if you need to “fix” the stability of a protein or the rate of its native or intermediate state formation? Having studied a large number of protein mutant forms, we have established the effect of various amino acid substitutions on the energy landscape of the protein. As a result, we have revealed a number of patterns to help researchers identify amino acid residues that determine the folding rate and the stability of globular proteins states and design a mutant form of a protein with desired properties.

Autosomal Recessive Cerebellar Atrophy and Spastic Ataxia in Patients With Pathogenic Biallelic Variants in GEMIN5

The hereditary ataxias are a heterogenous group of disorders with an increasing number of causative genes being described. Due to the clinical and genetic heterogeneity seen in these conditions, the majority of such individuals endure a diagnostic odyssey or remain undiagnosed. Defining the molecular etiology can bring insights into the responsible molecular pathways and eventually the identification of therapeutic targets. Here, we describe the identification of biallelic variants in the GEMIN5 gene among seven unrelated families with nine affected individuals presenting with spastic ataxia and cerebellar atrophy. GEMIN5, an RNA-binding protein, has been shown to regulate transcription and translation machinery. GEMIN5 is a component of small nuclear ribonucleoprotein (snRNP) complexes and helps in the assembly of the spliceosome complexes. We found that biallelic GEMIN5 variants cause structural abnormalities in the encoded protein and reduce expression of snRNP complex proteins in patient cells compared with unaffected controls. Finally, knocking out endogenous Gemin5 in mice caused early embryonic lethality, suggesting that Gemin5 expression is crucial for normal development. Our work further expands on the phenotypic spectrum associated with GEMIN5-related disease and implicates the role of GEMIN5 among patients with spastic ataxia, cerebellar atrophy, and motor predominant developmental delay.

Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL₅) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL₅ ↔ FL₅ mechanism, in which the final helical state, FL₅, forms from IL₅ with a time constant of 50-200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.

Thermodynamics of hydrophobic-polar model proteins on the face-centered cubic lattice

The HP model, a coarse-grained protein representation with only hydrophobic (H) and polar (P) amino acids, has already been extensively studied on the simple cubic (SC) lattice. However, this geometry severely restricts possible bond angles, and a simple improvement is to instead use the face-centered cubic (fcc) lattice. In this paper, the density of states and ground state energies are calculated for several benchmark HP sequences on the fcc lattice using the replica-exchange Wang-Landau algorithm and a powerful set of Monte Carlo trial moves. Results from the fcc lattice proteins are directly compared with those obtained from a previous lattice protein folding study with a similar methodology on the SC lattice. A thermodynamic analysis shows comparable folding behavior between the two lattice geometries, but with a greater rate of hydrophobic-core formation persisting into lower temperatures on the fcc lattice.

Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

Apart from being the most common mechanism of regulating protein function and transmitting signals throughout the cell, phosphorylation has an ability to induce disorder-to-order transition in an intrinsically disordered protein. In particular, it was shown that folding of the intrinsically disordered protein, eIF4E-binding protein isoform 2 (4E-BP2), can be induced by multisite phosphorylation. Here, the principles that govern the folding of phosphorylated 4E-BP2 (pT37pT46 4E-BP2_18-62) are investigated by analyzing canonical and replica exchange molecular dynamics trajectories, generated with the coarse-grained united-residue force field, in terms of local and global motions and the time dependence of formation of contacts between C^αs of selected pairs of residues. The key residues involved in the folding of the pT37pT46 4E-BP2_18-62 are elucidated by this analysis. The correlations between local and global motions are identified. Moreover, for a better understanding of the physics of the formation of the folded state, the experimental structure of the pT37pT46 4E-BP2_18-62 is analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. It is shown that without molecular dynamics simulations the kinks are able to identify not only the phosphorylated sites of protein, the key players in folding, but also the reasons for the weak stability of the pT37pT46 4E-BP2_18-62.

A Novel Branch-and-Bound Algorithm for the Protein Folding Problem in the 3D HP Model

The protein folding problem (PFP) is an important issue in bioinformatics and biochemical physics. One of the most widely studied models of protein folding is the hydrophobic-polar (HP) model introduced by Dill. The PFP in the three-dimensional (3D) lattice HP model has been shown to be NP-complete; the proposed algorithms for solving the problem can therefore only find near-optimal energy structures for most long benchmark sequences within acceptable time periods. In this paper, we propose a novel algorithm based on the branch-and-bound approach to solve the PFP in the 3D lattice HP model. For 10 48-monomer benchmark sequences, our proposed algorithm finds the lowest energies so far within comparable computation times than previous methods.

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain

Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in ∼15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of β-strands in folding, misfolding, and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D, and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. We show that the formation of each β-strand in folding trajectories is accompanied by the emergence of kinks in internal coordinate space as well as a decrease in local free energy. In particular, the decrease in downhill folding trajectory is ∼7 kcal/mol, while it varies between 31 and 48 kcal/mol for the three-state folding trajectory. The kink analyses of the experimental structures give new insights into formation of intermediates, which may become a useful tool for preventing aggregation.

Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes

The "fitness" landscapes of genetic sequences are characterized by high dimensionality and "ruggedness" due to sign epistasis. Ascending from low to high fitness on such landscapes can be difficult because adaptive trajectories get stuck at low-fitness local peaks. Compounding matters, recent theoretical arguments have proposed that extremely long, winding adaptive paths may be required to reach even local peaks: a "maze-like" landscape topography. The extent to which peaks and mazes shape the mode and tempo of evolution is poorly understood, due to empirical limitations and the abstractness of many landscape models. We explore the prevalence, scale, and evolutionary consequences of landscape mazes in a biophysically grounded computational model of protein evolution that captures the "frustration" between "stability" and aggregation propensity. Our stability-aggregation landscape exhibits extensive sign epistasis and local peaks galore. Although this frequently obstructs adaptive ascent to high fitness and virtually eliminates reproducibility of evolutionary outcomes, many adaptive paths do successfully complete the ascent from low to high fitness, with hydrophobicity a critical mediator of success. These successful paths exhibit maze-like properties on a global landscape scale, in which taking an indirect path helps to avoid low-fitness local peaks. This delicate balance of "hard but possible" adaptation could occur more broadly in other biological settings where competing interactions and frustration are important.

Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1

Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that recognizes post-transcriptionally abnormal transcripts and mediates their degradation. The master regulator of NMD is UPF1, an enzyme with intrinsic ATPase and helicase activities. The cancer genomic sequencing data has identified frequently mutated residues in the CH-domain and ATP-binding site of UPF1. In silico screening of UPF1 stability change as a function over 41 cancer mutations has identified five variants with significant effects: K164R, R253W, T499M, E637K, and E833K. To explore the effects of these mutations on the associated energy landscape of UPF1, molecular dynamics simulations (MDS) were performed. MDS identified stable H-bonds between residues S152, S203, S205, Q230/R703, and UPF2/AMPPNP, and suggest that phosphorylation of Serine residues may control UPF1-UPF2 binding. Moreover, the alleles K164R and R253W in the CH-domain improved UPF1-UPF2 binding. In addition, E637K and E833K alleles exhibited improved UPF1-AMPPNP binding compared to the T499M variant; the lower binding is predicted from hindrance caused by the side-chain of T499M to the docking of the tri-phosphate moiety (AMPPNP) into the substrate site. The dynamics of wild-type/mutant systems highlights the flexible nature of the ATP-binding region in UPF1. These insights can facilitate the development of drug discovery strategies for manipulating NMD signaling in cell systems using chemical tools.

The Urfold: Structural similarity just above the superfold level?

We suspect that there is a level of granularity of protein structure intermediate between the classical levels of "architecture" and "topology," as reflected in such phenomena as extensive three-dimensional structural similarity above the level of (super)folds. Here, we examine this notion of architectural identity despite topological variability, starting with a concept that we call the "Urfold." We believe that this model could offer a new conceptual approach for protein structural analysis and classification: indeed, the Urfold concept may help reconcile various phenomena that have been frequently recognized or debated for years, such as the precise meaning of "significant" structural overlap and the degree of continuity of fold space. More broadly, the role of structural similarity in sequence↔structure↔function evolution has been studied via many models over the years; by addressing a conceptual gap that we believe exists between the architecture and topology levels of structural classification schemes, the Urfold eventually may help synthesize these models into a generalized, consistent framework. Here, we begin by qualitatively introducing the concept.

A look back at the molten globule state of proteins: thermodynamic aspects

Interest in protein folding intermediates lies in their significance to protein folding pathways. The molten globule (MG) state is one such intermediate lying on the kinetic (and sometimes thermodynamic) pathway between native and unfolded states. Development of our qualitative and quantitative understanding of the MG state can provide deeper insight into the folding pathways and hence potentially facilitate solution of the protein folding problem. An extensive look at literature suggests that most studies into protein MG states have been largely qualitative. Attempts to obtain quantitative insights into MG states have involved application of high-sensitivity calorimetry (differential scanning calorimetry and isothermal titration calorimetry). This review addresses the progress made in this direction by discussing the knowledge gained to date, along with the future promise of calorimetry, in providing quantitative information on the structural features of MG states. Particular attention is paid to the question of whether such states share common structural features or not. The difference in the nature of the transition from the MG state to the unfolded state, in terms of cooperativity, has also been addressed and discussed.

Autonomous Sequences in Myoglobin Emerging from X-ray Structure of Holomyoglobin

The proposed continuous folding structure units are fundamental to analyze protein structure. Here, we could elucidate for the first time two types of hydrophobic core networks in apomyoglobin using continuous folding structure units. In myoglobin, two autonomous sequences emerged clearly. We could thus characterize the autonomous sequences using well-defined hydrophobic core networks within respective semifolds. A hydrophobic core is defined as a pair of topology-local hydrophobic amino acids in different folding structures. Hydrophobic core formation is indispensable to stabilize the different folding structures via an efficient hydrophobic interaction. Autonomous sequences in myoglobin encode tertiary structure information for semifolds. These sequences fold autonomously into small sets of continuous folding structure units to grow separate semifolds on each separate framework. The autonomous sequence can be defined as the local sequence assigned to the small set of continuous folding structure units. They create the discrete hydrophobic region in a semifold by assembly of their hydrophobic regions. Semifolds were characterized by discrete hydrophobic regions stabilized by respective type I hydrophobic core networks, which were present within each semifold. The discrete hydrophobic region of a semifold propagated itself with that of a different semifold by hydrophobic interactions in type II hydrophobic core network, which was present between different semifolds, as observed by the X-ray structures of semifolds. The most significant feature of semifolds in apomyoglobin was that they could be verified by the X-ray structure of holomyoglobin regardless of the instability of folds characteristic to autonomous sequence fragments. This work presents the first description of autonomous sequences.

The role of solvent quality and chain stiffness on the end-to-end contact kinetics of semiflexible polymers

Motivated by loop closure during protein folding and DNA packing, we systemically studied the effects of the solvent quality and chain stiffness on the thermodynamics and kinetics of the end-to-end contact formation for semiflexible polymer chains with reactive ends by Langevin dynamics simulations. In thermodynamics, a rich variety of products of the end-to-end contact have been discovered, such as loop, hairpin, toroid, and rodlike bundle, the populations of which are dependent on the solvent quality and chain stiffness. In kinetics, the overall pathways to form the end-to-end contact have been identified. The change of solvent quality and chain stiffness can tune the roughness of energy landscape and modulate the kinetic partitioning of the end-to-end contact formation pathways, leading to differing kinetic behaviors. In good or poor solvents, the first end-to-end contact rate k _c decreases with increasing the strength of bending stiffness k _θ monotonically. In very poor solvents, however, the dependence of the logarithm of the first end-to-end contact rate ln k _c on k _θ exhibits erratic behavior, which stems from more rugged energy landscape due to the polymer chain getting trapped into the intermediate state composed of the rodlike bundles with two ends in separation. For semiflexible chains, with increasing chain length N, the rate k _c increases initially and then decreases: in good solvents, the rate k _c exhibits a power-law relationship to chain length N with an exponent of ∼-1.50 in the region of long chains, which is in good agreement with the value derived from the experiment in the asymptotic limit of large N; and in poor solvents, the rate k _c exhibits a significantly stronger chain length dependence than those observed in good solvents in the region of long chains due to frustration to form the end-to-end contact along a specific path, especially the scaling exponent between the rate k _c and chain length N is ∼-3.62 for the case of polymer chains with k _θ = 4 at the solvent quality ε _ij = 1, in accord with the value obtained from the experiments.

Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape

A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths-the rare trajectories that transit between the folded and unfolded ensembles-using only thermodynamic information, such as a low-dimensional equilibrium free-energy landscape. However, commonly used one-dimensional landscapes typically fall short of this aim, because an empirical coordinate-dependent diffusion coefficient has to be fit to transition-path trajectory data in order to reproduce the transition-path dynamics. We show that an alternative, first-principles free-energy landscape predicts transition-path statistics that agree well with simulations and single-molecule experiments without requiring dynamical data as an input. This "topological configuration" model assumes that distinct, native-like substructures assemble on a time scale that is slower than native-contact formation but faster than the folding of the entire protein. Using only equilibrium simulation data to determine the free energies of these coarse-grained intermediate states, we predict a broad distribution of transition-path transit times that agrees well with the transition-path durations observed in simulations. We further show that both the distribution of finite-time displacements on a one-dimensional order parameter and the ensemble of transition-path trajectories generated by the model are consistent with the simulated transition paths. These results indicate that a landscape based on transient folding intermediates, which are often hidden by one-dimensional projections, can form the basis of a predictive model of protein-folding transition-path dynamics.

Universal folding pathways of polyhedron nets

Low-dimensional objects such as molecular strands, ladders, and sheets have intrinsic features that affect their propensity to fold into 3D objects. Understanding this relationship remains a challenge for de novo design of functional structures. Using molecular dynamics simulations, we investigate the refolding of the 24 possible 2D unfoldings ("nets") of the three simplest Platonic shapes and demonstrate that attributes of a net's topology-net compactness and leaves on the cutting graph-correlate with thermodynamic folding propensity. To explain these correlations we exhaustively enumerate the pathways followed by nets during folding and identify a crossover temperature [Formula: see text] below which nets fold via nonnative contacts (bonds must break before the net can fold completely) and above which nets fold via native contacts (newly formed bonds are also present in the folded structure). Folding above [Formula: see text] shows a universal balance between reduction of entropy via the elimination of internal degrees of freedom when bonds are formed and gain in potential energy via local, cooperative edge binding. Exploiting this universality, we devised a numerical method to efficiently compute all high-temperature folding pathways for any net, allowing us to predict, among the combined 86,760 nets for the remaining Platonic solids, those with highest folding propensity. Our results provide a general heuristic for the design of 2D objects to stochastically fold into target 3D geometries and suggest a mechanism by which geometry and folding propensity are related above [Formula: see text], where native bonds dominate folding.

Effect of Cation-π Interaction on Macroionic Self-Assembly

A series of rod-shaped polyoxometalates (POMs) [Bu4 N]7 [Mo6 O18 NC(CH2 O)3 MnMo6 O18 (OCH2 )3 CNMo6 O18 ] and [Bu4 N]7 [ArNMo6 O17 NC(CH2 O)3 MnMo6 O18 (OCH2 )3 CNMo6 O17 NAr] (Ar=2,6-dimethylphenyl, naphthyl and 1-methylnaphthyl) were chosen to study the effects of cation-π interaction on macroionic self-assembly. Diffusion ordered spectroscopy (DOSY) and isothermal titration calorimetry (ITC) techniques show that the binding affinity between the POMs and Zn2+ ions is enhanced significantly after grafting aromatic groups onto the clusters, leading to the effective replacement of tetrabutylammonium counterions (TBAs) upon the addition of ZnCl2 . The incorporation of aromatic groups results in the significant contribution of cation-π interaction to the self-assembly, as confirmed by the opposite trend of assembly size vs. ionic strength when compared with those without aromatic groups. The small difference between two aromatic groups toward the Zn2+ ions is amplified after combining with the clusters, which consequently triggers the self-recognition behavior between two highly similar macroanions.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method.

Synthesis of luminescent lanthanide complexes within crosslinked protein crystal matrices

Eu(TTA)₃phen was synthesized inside of crosslinked protein crystals. And we characterized the volumetric changes quantitatively induced by DMSO.

Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition

Using multi-site time-resolved FRET, it is shown that equilibrium unfolding of monellin is not only heterogeneous, but that the degree of non-cooperativity differs between the sole α-helix and different parts of the β-sheet.

Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod

X-ray structural determination of segments of the myosin rod has proved difficult because of the strong salt-dependent aggregation properties and repeating pattern of charges on the surface of the coiled-coil that lead to the formation of paracrystals. This problem has been resolved in part through the use of globular assembly domains that improve protein folding and prevent aggregation. The primary consideration now in designing coiled-coil fusion constructs for myosin is deciding where to truncate the coiled-coil and which amino acid residues to include from the folding domain. This is especially important for myosin that contains numerous regions of low predicted coiled-coil propensity. Here we describe the strategy adopted to determine the structure of the region that extends from Arg1677 - Leu1797 that included two areas that do not show a strong sequence signature of a conventional left-handed coiled coil or canonical heptad repeat. This demonstrates again that, with careful choice of fusion constructs, overlapping structures exhibit very similar conformations for the myosin rod fragments in the canonical regions. However, conformational variability is seen around Leu1706 which is a hot spot for cardiomyopathy mutations suggesting that this might be important for function.

Structure-Based Prediction of Protein-Folding Transition Paths

We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each transient state corresponds to the assembly of one or more discrete, cooperative units, which are determined directly from the native structure. We show that the transition state on a folding pathway is reached when a small number of critical contacts are formed between a specific set of substructures, after which folding proceeds downhill in free energy. This approach suggests a natural resolution for distinguishing parallel folding pathways and provides a simple means to predict the rate-limiting step in a folding reaction. Our theory identifies a common folding mechanism for proteins with diverse native structures and establishes general principles for the self-assembly of polymers with specific interactions.

On Stable States in a Topologically Driven Protein Folding Model

Theoretical models of protein folding often make simplifying assumptions that allow analysis, yielding interesting theoretical results. In this article, we study models where folding dynamics is primarily driven by local topological features in an iterative manner. We illustrate the merit of the proposed approach through its ability to simulate realistic protein folding processes even when the sequence content information is reduced to just hydrophobic and polar. We then analyze our models and show that under our simple assumptions, certain structures are inherently unstable, and that determining whether structures can be stable is an [Formula: see text]-hard problem. Interestingly, we find that when our model has only two amino acids, the problem becomes solvable in polynomial time.

EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction

BACKGROUND

Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify relevant regions of the solution space, i.e. correct contacts. Every additional source of information can contribute to narrowing down candidate regions. Therefore, recent methods combined evolutionary and sequence-based information as well as evolutionary and physicochemical information. We develop a new contact predictor (EPSILON-CP) that goes beyond current methods by combining evolutionary, physicochemical, and sequence-based information. The problems resulting from the increased dimensionality and complexity of the learning problem are combated with a careful feature analysis, which results in a drastically reduced feature set. The different information sources are combined using deep neural networks.

RESULTS

On 21 hard CASP11 FM targets, EPSILON-CP achieves a mean precision of 35.7% for top- L/10 predicted long-range contacts, which is 11% better than the CASP11 winning version of MetaPSICOV. The improvement on 1.5L is 17%. Furthermore, in this study we find that the amino acid composition, a commonly used feature, is rendered ineffective in the context of meta approaches. The size of the refined feature set decreased by 75%, enabling a significant increase in training data for machine learning, contributing significantly to the observed improvements.

CONCLUSIONS

Exploiting as much and diverse information as possible is key to accurate contact prediction. Simply merging the information introduces new challenges. Our study suggests that critical feature analysis can improve the performance of contact prediction methods that combine multiple information sources. EPSILON-CP is available as a webservice: http://compbio.robotics.tu-berlin.de/epsilon/.

Silicone oil promotes amyloid-like aggregation of αB-crystallin

Silicone oil induced changes of secondary structures of αB-crystallin (CRYAB) and promoted its aggregation into amyloid-like nanostructures.

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Protein Folding Structures: Formation of Folding Structures Based on Probability Theory

To the best of our knowledge, this is the first study that shows that the X-ray structures of proteins can be dissected into their continuous folding structure units. Each folding structure unit was designed such that both the terminal di- or tri-peptide sequences shared common sequences with the two adjacent folding structure units. To encode the folding structure information of proteins into their amino acid sequences, we proposed 44 kinds of folding elements, which covered all of the amino acids in the protein chains, and defined all folding structure units. The folding element was defined to mean a minimum structural piece, which covered the frame of the main chain of each amino acid in a protein chain. A folding structure unit of a local sequence could be fully characterized by the sequential combination of individual folding elements assigned to each amino acid. The folding structure information showed amino acid preferences in various positions in folding structure units. Folding structure formation proceeded on the basis of probability theory. Strikingly, relative formation ability analysis clearly indicated that we can decode the types and the chain length of folding structure units from the amino acid sequence of a protein.