Early Folding Intermediates Research Articles

Formation of the Native Topology of a Protein is due to the "Conserved but Non-Functional" Residues: A Case of Apomyoglobin Folding.

This paper is dedicated to the memory of Oleg B. Ptitsyn (1929-1999) and presents an answer to his question: "What is the role of conserved non-functional residues in protein folding?". This answer follows from the experimental works of three labs. The role of non-functional but conserved residues of apomyoglobin (apoMb) in the formation of the native protein fold in the molten globule state has been experimentally revealed. This research proves that the non-functional but conserved residues of apoMb are necessary for the formation and maintenance of the correct topological arrangement of the main elements in the apoMb secondary structure already in the early folding intermediate.

A multipoint guidance mechanism for β-barrel folding on the SAM complex.

Mitochondrial β-barrel proteins are essential for the transport of metabolites, ions and proteins. The sorting and assembly machinery (SAM) mediates their folding and membrane insertion. We report the cryo-electron microscopy structure of the yeast SAM complex carrying an early eukaryotic β-barrel folding intermediate. The lateral gate of Sam50 is wide open and pairs with the last β-strand (β-signal) of the substrate-the 19-β-stranded Tom40 precursor-to form a hybrid barrel in the membrane plane. The Tom40 barrel grows and curves, guided by an extended bridge with Sam50. Tom40's first β-segment (β1) penetrates into the nascent barrel, interacting with its inner wall. The Tom40 amino-terminal segment then displaces β1 to promote its pairing with Tom40's last β-strand to complete barrel formation with the assistance of Sam37's dynamic α-protrusion. Our study thus reveals a multipoint guidance mechanism for mitochondrial β-barrel folding.

TorsinA folding and N-linked glycosylation are sensitive to redox homeostasis

The Endoplasmic Reticulum (ER) is responsible for the folding and post-translational modification of secretory proteins, as well as for triaging misfolded proteins. During folding, there is a complex yet only partially understood interplay between disulfide bond formation, which is an enzyme catalyzed event in the oxidizing environment of the ER, along with other post-translational modifications (PTMs) and chaperone-supported protein folding. Here, we used the glycoprotein torsinA as a model substrate to explore the impact of ER redox homeostasis on PTMs and protein biogenesis. TorsinA is a AAA+ ATPase with unusual oligomeric properties and controversial functions. The deletion of a C-terminal glutamic acid residue (∆E) is associated with the development of Early-Onset Torsion Dystonia, a severe movement disorder. TorsinA differs from other AAA+ ATPases since it is an ER resident, and as a result of its entry into the ER torsinA contains two N-linked glycans and at least one disulfide bond. The role of these PTMs on torsinA biogenesis and function and the identity of the enzymes that catalyze them are poorly defined. Using a yeast torsinA expression system, we demonstrate that a specific protein disulfide isomerase, Pdi1, affects the folding and N-linked glycosylation of torsinA and torsinA∆E in a redox-dependent manner, suggesting that the acquisition of early torsinA folding intermediates is sensitive to perturbed interactions between Cys residues and the quality control machinery. We also highlight the role of specific Cys residues during torsinA biogenesis and demonstrate that torsinA∆E is more sensitive than torsinA when these Cys residues are mutated.

Molecular Assembly Pathway of Mitochondrial SAM50 in Native Membranes

The major outer mitochondrial membrane chaperone is the Sorting and Assembly Machinery (SAM). SAM is a trimeric complex, with the transmembrane β-barrel Sam50 forming the core component. It functions in the sorting and trafficking of β-barrel precursors into the mitochondrial outer membrane, and thus is indispensable for cell survival. Details of the energetics governing the structure and function of the SAM complex, and the explicit molecular role(s) of Sam50 still need to be unraveled. Using a consolidated approach involving thermodynamic and kinetic measurements, we now deduce unprecedented molecular insight on the assembly of Sam50 in native membranes. We measure the per-residue contribution of the Sam50 primary sequence to its folding and thermodynamic stability, using an exhaustive alanine scanning mutagenesis strategy in phosphatidylethanolamine-doped phosphatidylcholine-rich membranes. Our findings using ϕ-value analysis reveal two on-pathway early kinetic folding intermediates that populate prior to the complete assembly of Sam50 in the lipid bilayer. The early intermediates possess structured N- and C-terminal strands, whereas the central strands remain unfolded or form non-native contacts. We observe a β-augmentation mechanism involving the pre-folded terminal strands in the late intermediate, which is followed by a slow rearrangement process to yield a folded and functional Sam50 β-barrel. Measurements of thermodynamic stability of the end-state β-barrel reveal localized destabilization of the N-terminal strands and a scaffold anchoring role for the C-terminal region, which bear direct implications in the chaperoning mechanism of Sam50. By linking our findings from per-residue energetics with the mechanism of Sam50 action, we provide a thermodynamic perspective for Sam50 function in mitochondria.

Do folding elements trade‐off with function in the human mitochondrial metabolite transporter?

In humans, transmembrane β‐barrels are found exclusively in the outer mitochondrial membrane (OMM). They comprise metabolite transporters, translocases, and chaperones, which together control cellular homeostasis. The metabolite transporters — known as voltage‐dependent anion channels (VDACs) – are the most abundant OMM barrels. They are 19‐stranded β‐barrel structures that also form important pharmacological targets due to their roles in metabolite flux, steroidogenesis, gametogenesis, and ROS regulation. Despite long‐standing efforts, molecular factors that regulate VDAC function and folding at the atomistic level are not known. Here, we map the folding nucleus and the assembly pathway of human VDAC isoform 2 in phosphocholine vesicles. We carry out a comprehensive measurement of hVDAC2 folding kinetics, and equilibrium thermodynamic contribution, of each of the 270 non‐Ala residues of the 294‐residue barrel. Interestingly, we obtain a two‐state thermodynamic equilibrium that is attained through two detectable on‐pathway early folding intermediates, which are assembled in milliseconds – seconds. These intermediates undergo slow conformational restructuring to form the folded VDAC2 barrel. We find that specific charged residues that form a part of these early intermediates also positively regulate the gating characteristics of VDAC2. This observation is unprecedented, as directed evolution of protein sequences in favor of function usually place a stability burden on its structure that additionally impedes protein assembly. Our findings provide molecular insight on the assembly pathway of human VDAC2, and directly link these folding elements with VDAC2 function as the metabolite transporter of human mitochondria.Support or Funding InformationThis work was supported by the Wellcome Trust/DBT India Alliance Fellowship [grant number IA/I/14/1/501305] awarded to RM.

Linking Folding Landscape with Function in the Human Mitochondrial VDAC2

Transmembrane β-barrels in humans are exclusive to the mitochondrial outer membrane (OMM). They include translocases, porins, and chaperones, which together regulate cellular homeostasis. The most abundant OMM proteins are the voltage-dependent anion channels (VDACs), which are 19-stranded multifunctional metabolite flux porins that are also important pharmacological targets. In humans, VDAC2 is anti-apoptotic and functions additionally in metabolite flux, steroidogenesis, gametogenesis, and ROS regulation, making this isoform indispensable for the cell. Despite long-standing efforts, molecular elements regulating VDAC function and folding are not known. Here, we map the folding nucleus and the assembly pathway of human VDAC2 in phosphocholine vesicles. We carry out a comprehensive measurement of folding kinetics and equilibrium thermodynamic contribution of each of the 270 non-Ala residues in the 294-residue barrel. Interestingly, we obtain a two-state thermodynamic equilibrium that is achieved through two detectable on-pathway early folding intermediates, which drive barrel assembly. Detailed analysis of the transition state structure reveals that specific strands at the N-terminal and central region of the barrel assemble first, which is followed by structuring of the C-terminal region. Residues causing frustration in the folding (Φ-value < 0) are more populated towards the C-terminal strands. Furthermore, specific charged residues that regulate the gating characteristics of human VDAC2 are surprisingly a part of the folding nucleus. The only interesting exception is D169, which is functionally important in vivo for cell survival, but establishes non-native contacts during VDAC2 folding. Relating our findings with the proposed mechanism of chaperone–assisted folding in the OMM provides molecular insight that links the assembly pathway of human VDAC2 with function.

Abstract 4798: Targeting hTERT for treatment of glioblastoma (GBM)

Abstract Approximately 86% of GBM tumors exhibit a mutation at -124 or -146 bp upstream from the ATG start site in the transcription activating promoter region of Human telomerase reverse transcriptase (hTERT). Mutations in the hTERT promoter are known to impair repression, leading to overexpression of hTERT and tumor maintenance. Yet, complete understanding of mechanistic implications is still necessary. While overexpressed hTERT is associated with oncogenesis and resistance to apoptosis, we also observe phenotypes unrelated to the reverse transcription function. We characterized long-term glioma cell lines and glioma PDX models by hTERT promoter mutation status, hTERT mRNA expression, and hTERT protein expression in subcellular fractions. The -124 and -146 mutations are located in the major 5-12 G-quadruplex and result in misfolding of the silencer element, thus causing over-expression of hTERT. Using a diverse small molecule library, we identified a small drug-like pharmacological chaperone (pharmacoperone) molecule, TG-4260, which binds to the 26 mer base-pair heteroduplex loop, which is the nucleation site for cooperative folding of the major 5-12 G-quadruplex. The chaperone effect of TG-4260 corrects DNA hTERT G-quadruplex misfolding resulting from the promoter mutations and restores the silencer function of the G-quadruplex. TG-4260 directly decreases the transcription activity of the −124, −124/125, −138/139, and −146 mutants to a similar extent and suppresses the downstream gene BCL2, which activates caspase-3 and produces cell-cycle arrest, leading to cell death. This is the first example of the use of a pharmacoperone molecule to correct the misfolding of a DNA G-quadruplex element resulting from mutations in an early folding intermediate. We screened GBM cell models against this novel small molecule inhibitor that interferes with mutated hTERT promoter and demonstrated that TG-4260 selectively suppresses glioma cell viability without affecting non-transformed normal human astrocytes. Finally, telomere phenotypes from treated cells indicate non-canonical functions of telomerase may also contribute to glioma pathogenesis. Citation Format: Saumya Reddy Bollam, Hyun-Jin Kang, Sen Peng, Vijay Gokhale, Laurence Hurley, Michael Berens, Harshil Dhruv. Targeting hTERT for treatment of glioblastoma (GBM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4798.

A two-domain folding intermediate of RuBisCO in complex with the GroEL chaperonin

The chaperonins (GroEL and GroES in Escherichia coli) are ubiquitous molecular chaperones that assist a subset of essential substrate proteins to undergo productive folding to the native state. Using single particle cryo EM and image processing we have examined complexes of E. coli GroEL with the stringently GroE-dependent substrate enzyme RuBisCO from Rhodospirillum rubrum. Here we present snapshots of non-native RuBisCO - GroEL complexes. We observe two distinct substrate densities in the binary complex reminiscent of the two-domain structure of the RuBisCO subunit, so that this may represent a captured form of an early folding intermediate. The occupancy of the complex is consistent with the negative cooperativity of GroEL with respect to substrate binding, in accordance with earlier mass spectroscopy studies.

Folding of maltose binding protein outside of and in GroEL

We used hydrogen exchange-mass spectrometry (HX MS) and fluorescence to compare the folding of maltose binding protein (MBP) in free solution and in the GroEL/ES cavity. Upon refolding, MBP initially collapses into a dynamic molten globule-like ensemble, then forms an obligatory on-pathway native-like folding intermediate (1.2 seconds) that brings together sequentially remote segments and then folds globally after a long delay (30 seconds). A single valine to glycine mutation imposes a definable folding defect, slows early intermediate formation by 20-fold, and therefore subsequent global folding by approximately twofold. Simple encapsulation within GroEL repairs the folding defect and reestablishes fast folding, with or without ATP-driven cycling. Further examination exposes the structural mechanism. The early folding intermediate is stabilized by an organized cluster of 24 hydrophobic side chains. The cluster preexists in the collapsed ensemble before the H-bond formation seen by HX MS. The V9G mutation slows folding by disrupting the preintermediate cluster. GroEL restores wild-type folding rates by restabilizing the preintermediate, perhaps by a nonspecific equilibrium compression effect within its tightly confining central cavity. These results reveal an active GroEL function other than previously proposed mechanisms, suggesting that GroEL possesses different functionalities that are able to relieve different folding problems. The discovery of the preintermediate, its mutational destabilization, and its restoration by GroEL encapsulation was made possible by the measurement of a previously unexpected type of low-level HX protection, apparently not dependent on H-bonding, that may be characteristic of proteins in confined spaces.

Substrate specificity in the context of molecular chaperones.

Molecular chaperones are one of the key players in protein biology and as such their structure and mechanism of action have been extensively studied. However the substrate specificity of molecular chaperones has not been well investigated. This review aims to summarize what is known about the substrate specificity and substrate recognition motifs of chaperones so as to better understand what substrate specificity means in the context of molecular chaperones. Available literature shows that the majority of chaperones have broad substrate range and recognize non-native conformations of proteins depending on recognition of hydrophobic and/or charged patches. Based on these recognition motifs chaperones can select for early, mid or late folding intermediates. Another major contributor to chaperone specificity are the co-chaperones they interact with as well as the sub-cellular location they are expressed in and the inducability of their expression. Some chaperones which have only one or a few known substrates are reported. In their case the mode of recognition seems to be specific structural complementarity between chaperone and substrate. It can be concluded that the vast majority of chaperones do not show a high degree of specificity but recognize elements that signal non-native protein conformation and their substrate range is modulated by the context they function in. However a few chaperones are known that display exquisite specificity of their substrate e.g. mammalian heat shock protein 47 collagen interaction. © 2017 IUBMB Life, 69(9):647-659, 2017.

Abstract 1169: mtTERT promoter as a target for treatment of glioblastoma

Abstract Approximately 86% of GBM tumors exhibit mutation at -124 or -146 bases upstream of the ATG start site in the transcription activating promoter region of Human telomerase reverse transcriptase (hTERT). Mutation in the promoter region of hTERT impairs repression, leading to overexpression of hTERT; inappropriate hTERT is associated with oncogenesis, tumor maintenance, and resistance to apoptosis. We surveyed long-term glioma cell lines and glioma PDX models for mt-hTERT; mRNA and protein expression of hTERT were assessed by qPCR and western blot. The -124 and -146 mutations are located in the major 5-12 G-quadruplex and result in misfolding of the silencer element and consequent over-expression of hTERT. Using a diverse small molecule library, we identified a small drug-like pharmacological chaperone (pharmacoperone) molecule, TG-4260, which binds to the 26 mer base-pair heteroduplex loop, which is the nucleation site for cooperative folding of the major 5-12 G-quadruplex. The chaperone effect of TG-4260 corrects DNA hTERT G-quadruplex misfolding resulting from the somatic mutations and restores the silencer function of the G-quadruplex thereby reducing hTERT activity. TG-4260 directly decreases the transcription activity of the WT and the −124, −124/125, −138/139, and −146 mutants to a similar extent and suppresses the downstream gene BCL2, which activates caspase-3 and produces cell-cycle arrest, leading to cell death. Finally, TG-4260 significantly inhibits telomerase and shortens telomere length after five days of treatment and induces a senescence-like phenotype. This is the first example of the use of a pharmacoperone molecule to correct the misfolding of a DNA G-quadruplex element resulting from mutations in an early folding intermediate. Finally, we screened GBM cell models against a novel small molecule inhibitor that interferes with mutated hTERT promoter and demonstrated that TG-4260 selectively suppresses glioma cell viability without affecting non-transformed normal human astrocytes. Citation Format: Saumya R. Bollam, Harshil D. Dhruv, Hyun-Jin Kang, Sen Peng, Vijay Gokhale, Laurence Hurley, Michael Berens. mtTERT promoter as a target for treatment of glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1169. doi:10.1158/1538-7445.AM2017-1169

OS01.3 mtTERT promoter as a target for treatment of Glioblastoma

AbstractApproximately 86% of GBM tumors exhibit mutation at -124 or -146 bases upstream of the ATG start site in the transcription activating promoter region of Human telomerase reverse transcriptase (hTERT). Mutation in the promoter region of hTERT impairs repression, leading to overexpression of hTERT; inappropriate hTERT is associated with oncogenesis, tumor maintenance, and resistance to apoptosis. We surveyed long-term glioma cell lines and glioma PDX models for mt-hTERT; mRNA and protein expression of hTERT were assessed by qPCR and western blot. The -124 and -146 mutations are located in the major 5–12 G-quadruplex and result in misfolding of the silencer element and consequent over-expression of hTERT. Using a diverse small molecule library, we identified a small drug-like pharmacological chaperone (pharmacoperone) molecule, TG-4260, which binds to the 26 mer base-pair heteroduplex loop, which is the nucleation site for cooperative folding of the major 5–12 G-quadruplex. The chaperone effect of TG-4260 corrects DNA hTERT G-quadruplex misfolding resulting from the somatic mutations and restores the silencer function of the G-quadruplex thereby reducing hTERT activity. TG-4260 directly decreases the transcription activity of the WT and the −124, −124/125, −138/139, and −146 mutants to a similar extent and suppresses the downstream gene BCL2, which activates caspase-3 and produces cell-cycle arrest, leading to cell death. Finally, TG-4260 significantly inhibits telomerase and shortens telomere length after five days of treatment and induces a senescence-like phenotype. This is the first example of the use of a pharmacoperone molecule to correct the misfolding of a DNA G-quadruplex element resulting from mutations in an early folding intermediate. Finally, we screened GBM cell models against a novel small molecule inhibitor that interferes with mutated hTERT promoter and demonstrated that TG-4260 selectively suppresses glioma cell viability without affecting non-transformed normal human astrocytes.

Determination of Protein Folding Intermediate Structures Consistent with Data from Oxidative Footprinting Mass Spectrometry

The mapping of folding landscapes remains an important challenge in protein chemistry. Pulsed oxidative labeling of exposed residues and their detection via mass spectrometry provide new means of taking time-resolved “snapshots” of the structural changes that occur during protein folding. However, such experiments have been so far only interpreted qualitatively. Here, we report the detailed structural interpretation of mass spectrometry data from fast photochemical oxidation of proteins (FPOP) experiments at atomic resolution in a biased molecular dynamics approach. We are able to calculate structures of the early folding intermediate of the model system barstar that are fully consistent with FPOP data and Φ values. Furthermore, structures calculated with both FPOP data and Φ values are significantly less compact and have fewer helical residues than intermediate structures calculated with Φ values only. This improves the agreement with the experimental β-Tanford value and CD measurements. The restraints that we introduce facilitate the structural interpretation of FPOP data and provide new means for refined structure calculations of transiently sampled states on protein folding landscapes.

Observing and Characterizing Early Folding Intermediates of E.Coli Rnase H using Kinetic and Equilibrium Approaches

E. coli ribonuclease H has been an important model system for protein folding for many years. It has long been known that it folds through an intermediate (Icore) en route to the native state. However, because folding to Icore occurs on the fast millisecond timescale, and there is very little Icore populated under equilibrium conditions, key questions have remained unanswered: What is the nature of the folding pathway en route to Icore, and how well packed is Icore?In this work, a new ultrarapid mixing technique coupled with time-correlated single photon counting detection of intrinsic fluorescence allows observation of the millisecond folding to Icore, including new early intermediates formed along the way. Mutagenesis and hydrogen exchange methods provide structural information about these new early intermediates. Additionally, two equilibrium models of Icore are made and characterized, providing new insight into the nature of this intermediate. This work increases our knowledge about the folding pathway and energy landscape of an important protein folding model system, at a time- and size-scale that is amenable to comparison with protein folding simulations.

Probing the protein-folding mechanism using denaturant and temperature effects on rate constants

Protein folding has been extensively studied, but many questions remain regarding the mechanism. Characterizing early unstable intermediates and the high-free-energy transition state (TS) will help answer some of these. Here, we use effects of denaturants (urea, guanidinium chloride) and temperature on folding and unfolding rate constants and the overall equilibrium constant as probes of surface area changes in protein folding. We interpret denaturant kinetic m-values and activation heat capacity changes for 13 proteins to determine amounts of hydrocarbon and amide surface buried in folding to and from TS, and for complete folding. Predicted accessible surface area changes for complete folding agree in most cases with structurally determined values. We find that TS is advanced (50-90% of overall surface burial) and that the surface buried is disproportionately amide, demonstrating extensive formation of secondary structure in early intermediates. Models of possible pre-TS intermediates with all elements of the native secondary structure, created for several of these proteins, bury less amide and hydrocarbon surface than predicted for TS. Therefore, we propose that TS generally has both the native secondary structure and sufficient organization of other regions of the backbone to nucleate subsequent (post-TS) formation of tertiary interactions. The approach developed here provides proof of concept for the use of denaturants and other solutes as probes of amount and composition of the surface buried in coupled folding and other large conformational changes in TS and intermediates in protein processes.

Roles of Ubiquitin in Endoplasmic Reticulum-Associated Protein Degradation (ERAD)

In the secretory pathway, quality control for the correct folding of proteins is largely occurring in the endoplasmic reticulum (ER), at the earliest possible stage and in an environment where early folding intermediates mix with terminally misfolded species. An elaborate cellular mechanism aims at dividing the former from the latter and promotes the selective transport of misfolded species back into the cytosol, a step called retrotranslocation. During retrotranslocation proteins will become ubiquitinated on the cytosolic side of the ER membrane by dedicated machineries and will be targeted to the proteasome for degradation. The entire process, from protein recognition to final degradation, has been named ER-associated protein degradation, or simply ERAD. Ubiquitin has well known functions in aiding late steps of substrate retrotranslocation and in targeting substrates to the proteasome. Recent results show that several cytosolic machineries allow ubiquitinated substrates to undergo extensive remodeling, or processing, on their poly-ubiquitin chains (PUCs). Although still ill-defined, PUC processing might have a unique function for ERAD in that it might provide a mechanism to generate optimal PUCs for recognition by proteasomal ubiquitin receptors. Ubiquitination might also have a previously unanticipated role in quality control of ER membrane proteins. This review recapitulates the current knowledge and recent findings about ERAD-specific roles of ubiquitin.

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states and folding pathways. We reconcile these two pictures in a combined experimental and simulation study of acyl-coenzyme A binding protein (ACBP), a two-state folder (folding time ~10 ms) exhibiting residual unfolded-state structure, and a putative early folding intermediate. Using single-molecule FRET in conjunction with side-chain mutagenesis, we first demonstrate that the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-range structure that can be perturbed by discrete hydrophobic core mutations. We then employ ultrafast laminar-flow mixing experiments to study the folding kinetics of ACBP on the microsecond time scale. These studies, along with Trp-Cys quenching measurements of unfolded-state dynamics, suggest that unfolded-state structure forms on a surprisingly slow (~100 μs) time scale, and that sequence mutations strikingly perturb both time-resolved and equilibrium smFRET measurements in a similar way. A Markov state model (MSM) of the ACBP folding reaction, constructed from over 30 ms of molecular dynamics trajectory data, predicts a complex network of metastable stables, residual unfolded-state structure, and kinetics consistent with experiment but no well-defined intermediate preceding the main folding barrier. Taken together, these experimental and simulation results suggest that the previously characterized fast kinetic phase is not due to formation of a barrier-limited intermediate but rather to a more heterogeneous and slow acquisition of unfolded-state structure.

Large Is Fast, Small Is Tight: Determinants of Speed and Affinity in Subunit Capture by a Periplasmic Chaperone

The chaperone/usher pathway assembles surface virulence organelles of Gram-negative bacteria, consisting of fibers of linearly polymerized protein subunits. Fiber subunits are connected through ‘donor strand complementation’: each subunit completes the immunoglobulin (Ig)-like fold of the neighboring subunit by donating the seventh β-strand in trans. Whereas the folding of Ig domains is a fast first-order process, folding of Ig modules into the fiber conformation is a slow second-order process. Periplasmic chaperones separate this process in two parts by forming transient complexes with subunits. Interactions between chaperones and subunits are also based on the principle of donor strand complementation. In this study, we have performed mutagenesis of the binding motifs of the Caf1M chaperone and Caf1 capsular subunit from Yersinia pestis and analyzed the effect of the mutations on the structure, stability, and kinetics of Caf1M–Caf1 and Caf1–Caf1 interactions. The results suggest that a large hydrophobic effect combined with extensive main-chain hydrogen bonding enables Caf1M to rapidly bind an early folding intermediate of Caf1 and direct its partial folding. The switch from the Caf1M–Caf1 contact to the less hydrophobic, but considerably tighter and less dynamic Caf1–Caf1 contact occurs via the zip-out–zip-in donor strand exchange pathway with pocket 5 acting as the initiation site. Based on these findings, Caf1M was engineered to bind Caf1 faster, tighter, or both faster and tighter. To our knowledge, this is the first successful attempt to rationally design an assembly chaperone with improved chaperone function.

Minireview: Structural insights into early folding events using continuous‐flow time‐resolved small‐angle X‐ray scattering

Small-angle X-ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous-flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow-based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time-resolved SAXS and the synergy with ab initio structure prediction and molecular dynamics simulations are discussed.

The High-Resolution NMR Structure of the Early Folding Intermediate of the Thermus thermophilus Ribonuclease H

Elucidation of the high-resolution structures of folding intermediates is a necessary but difficult step toward the ultimate understanding of the mechanism of protein folding. Here, using hydrogen-exchange-directed protein engineering, we populated the folding intermediate of the Thermus thermophilus ribonuclease H, which forms before the rate-limiting transition state, by removing the unfolded regions of the intermediate, including an α-helix and two β-strands (51 folded residues). Using multidimensional NMR, we solved the structure of this intermediate mimic to an atomic resolution (backbone rmsd, 0.51 Å). It has a native-like backbone topology and shows some local deviations from the native structure, revealing that the structure of the folded region of an early folding intermediate can be as well defined as the native structure. The topological parameters calculated from the structures of the intermediate mimic and the native state predict that the intermediate should fold on a millisecond time scale or less and form much faster than the native state. Other factors that may lead to the slow folding of the native state and the accumulation of the intermediate before the rate-limiting transition state are also discussed.