How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations

Co-translational folding (CTF) facilitates correct folding in vivo, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional state. Here, to gain structural insights on the underlying mechanisms, we performed comparative molecular simulations of SufI that mimic CTF as well as refolding schemes. A CTF scheme that relied on a codon-based prediction of translational rates exhibited folding probability markedly higher than that by the refolding scheme. When the CTF schedule is speeded up, the success rate dropped. These agree with experiments. Structural investigation clarified that misfolding of the middle domain was much more frequent in the refolding scheme than that in the codon-based CTF scheme. The middle domain is less stable and can fold via interactions with the folded N-terminal domain. Folding pathway networks showed the codon-based CTF gives narrower pathways to the native state than the refolding scheme.     

Kinetic partitioning mechanism governs the folding of the third FnIII domain of tenascin-C: evidence at the single-molecule level

Statistical mechanics and molecular dynamics simulations proposed that the folding of proteins can follow multiple parallel pathways on a rugged energy landscape from unfolded state en route to their folded native states. Kinetic partitioning mechanism is one of the possible mechanisms underlying such complex folding dynamics. Here, we use single-molecule atomic force microscopy technique to directly probe the multiplicity of the folding pathways of the third fibronectin type III domain from the extracellular matrix protein tenascin-C (TNfn3). By stretching individual (TNfn3)₈ molecules, we forced TNfn3 domains to undergo mechanical unfolding and refolding cycles, allowing us to directly observe the folding pathways of TNfn3. We found that, after being mechanically unraveled and then relaxed to zero force, TNfn3 follows multiple parallel pathways to fold into their native states. The majority of TNfn3 fold into the native state in a simple two-state fashion, while a small percentage of TNfn3 were found to be trapped into kinetically stable folding intermediate states with well-defined three-dimensional structures. Furthermore, the folding of TNfn3 was also influenced by its neighboring TNfn3 domains. Complex misfolded states of TNfn3 were observed, possibly due to the formation of domain-swapped dimeric structures. Our studies revealed the ruggedness of the folding energy landscape of TNfn3 and provided direct experimental evidence that the folding dynamics of TNfn3 are governed by the kinetic partitioning mechanism. Our results demonstrated the unique capability of single-molecule AFM to probe the folding dynamics of proteins at the single-molecule level.     

Direct observation of active protein folding using lock-in force spectroscopy

Direct observation of the folding of a single polypeptide chain can provide important information about the thermodynamic states populated along its folding pathway. In this study, we present a lock-in force-spectroscopy technique that improves resolution of atomic-force microscopy force spectroscopy to 400 fN. Using this technique we show that immunoglobulin domain 4 from Dictyostelium discoideum filamin (ddFLN4) refolds against forces of ∼4 pN. Our data show folding of this domain proceeds directly from an extended state and no thermodynamically distinct collapsed state of the polypeptide before folding is populated. Folding of ddFLN4 under load proceeds via an intermediate state. Three-state folding allows ddFLN4 to fold against significantly larger forces than would be possible for a mere two-state folder. We present a general model for protein folding kinetics under load that can predict refolding forces based on chain-length and zero force refolding rate.     

Cell patterning technologies for organotypic tissue fabrication

Bottom-up tissue engineering technologies address two of the main limitations of top-down tissue engineering approaches: the control of mass transfer and the fabrication of a controlled and functional histoarchitecture. These emerging technologies encompass mesoscale (e.g. cell sheets, cell-laden hydrogels and 3D printing) and microscale technologies (e.g. inkjet printing and laser-assisted bioprinting), which are used to manipulate and assemble cell-laden building blocks whose thicknesses correspond to the diffusion limit of metabolites, and present the capacity for cell patterning with microscale precision, respectively. Here, we review recent technological advances and further discuss how these technologies are complementary, and could therefore be combined for the biofabrication of organotypic tissues either in vitro, thus serving as realistic tissue models, or within a clinic setting.     

Cell traction force and measurement methods

Cell traction forces (CTFs) are crucial to many biological processes such as inflammation, wound healing, angiogenesis, and metastasis. CTFs are generated by actomyosin interactions and actin polymerization and regulated by intracellular proteins such as alpha-smooth muscle actin (α-SMA) and soluble factors such as transforming growth factor-β (TGF-β). Once transmitted to the extracellular matrix (ECM) through stress fibers via focal adhesions, which are assemblies of ECM proteins, transmembrane receptors, and cytoplasmic structural and signaling proteins (e.g., integrins), CTFs direct many cellular functions, including cell migration, ECM organization, and mechanical signal generation. Various methods have been developed over the years to measure CTFs of both populations of cells and of single cells. At present, cell traction force microscopy (CTFM) is among the most efficient and reliable method for determining CTF field of an entire cell spreading on a two-dimensional (2D) substrate surface. There are currently three CTFM methods, each of which is unique in both how displacement field is extracted from images and how CTFs are subsequently estimated. A detailed review and comparison of these methods are presented. Future research should improve CTFM methods such that they can automatically track dynamic CTFs, thereby providing new insights into cell motility in response to altered biological conditions. In addition, research effort should be devoted to developing novel experimental and theoretical methods for determining CTFs in three-dimensional (3D) matrix, which better reflects physiological conditions than 2D substrate used in current CTFM methods.     

Topological frustration and the folding of interleukin-1 beta

The cytokine, interleukin-1beta (IL-1beta), adopts a beta-trefoil fold. It is known to be much slower folding than similarly sized proteins, despite having a low contact order. Proteins are sufficiently well designed that their folding is not dominated by local energetic traps. Therefore, protein models that encode only the folded structure and are energetically unfrustrated (Gō-type), can capture the essentials of the folding routes. We investigate the folding thermodynamics of IL-1beta using such a model and molecular dynamics (MD) simulations. We develop an enhanced sampling technique (a modified multicanonical method) to overcome the sampling problem caused by the slow folding. We find that IL-1beta has a broad and high free energy barrier. In addition, the protein fold causes intermediate unfolding and refolding of some native contacts within the protein along the folding trajectory. This "backtracking" occurs around the barrier region. Complex folds like the beta-trefoil fold and functional loops like the beta-bulge of IL-1beta can make some of the configuration space unavailable to the protein and cause topological frustration.     

Armored cuticular membranes in Brachycera (Insecta,Diptera)

This study describes and quantifies the ultrastructural design of some cuticular protuberances in the Diptera-Brachycera that appear to have a specialized mechanical function. The microsculpture of membranes in the transitional areas of prothorax-neck, neck-head, head-mouthparts, and in the articulations thorax-coxa and coxa-trochanter was investigated in eight species from six families (Tabanidae, Stratiomyidae, Calliphoridae, Syrphidae, Muscidae and Drosophilidae) by means of scanning electron microscopy. The membrane armatures are single or grouped microtrichia, often located on microplates in the flexible membrane. The different membranes were compared using the following details: microtrichia length, microplate length and width, the shortest distance between microplates, and the number of microtrichia per microplate. Five different types of microstructure were observed: (1) single short papilla-like microtrichia directly arising from the flexible membrane, (2) single elongated microtrichia directly arising from the flexible membrane, (3) single microtrichia located on small areas of the inflexible cuticle, here called microplates, (4) microtrichia groups located on the microplates, and (5) microplates without microtrichia in the flexible membrane. The study reveals the differences in the surface ultrastructure of membranes between different parts of body and between different taxa of flies. The prothorax-neck transition is less specialized in membrane armature as compared with the head-neck articulation, and especially with that of the head-proboscis. The head-proboscis transition has the most complex membrane armature of those species studied. The membrane of the basal joints of the legs has larger plates and a higher number of microtrichia per plate than that of the more distal joints. The complexity of the membrane armature depends on the dimensions of the animal: the smallest species have short ungrouped microtrichia or micropapillae, whereas large species have the highest degree of grouping, the longest microtrichia, and the largest microplates. Three main mechanical functions served by the different armored membranes are suggested, based on the specific characteristics of the microsculptural design: (1) fixation of the folds, (2) prevention of folding, and (3) determination of direction of folding. J. Morphol. 234:213–222, 1997. © 1997 Wiley-Liss, Inc.     

Fitting protein chains to cubic lattice is NP-complete

It is known that folding a protein chain into a cubic lattice is an NP-complete problem. We consider a seemingly easier problem: given a three-dimensional (3D) fold of a protein chain (coordinates of its C(alpha) atoms), we want to find the closest lattice approximation of this fold. This problem has been studied under names such as "lattice approximation of a protein chain", "the protein chain fitting problem", and "building of protein lattice models". We show that this problem is NP-complete for the cubic lattice with side close to 3.8 A and coordinate root mean square deviation.     

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

We perform a detailed analysis of the thermodynamics and folding kinetics of the SH3 domain fold with discrete molecular dynamic simulations. We propose a protein model that reproduces some of the experimentally observed thermodynamic and folding kinetic properties of proteins. Specifically, we use our model to study the transition state ensemble of the SH3 fold family of proteins, a set of unstable conformations that fold to the protein native state with probability 1/2. We analyze the participation of each secondary structure element formed at the transition state ensemble. We also identify the folding nucleus of the SH3 fold and test extensively its importance for folding kinetics. We predict that a set of amino acid contacts between the RT-loop and the distal hairpin are the critical folding nucleus of the SH3 fold and propose a hypothesis that explains this result.     

Glycogen synthase kinase-3beta regulates presenilin 1 C-terminal fragment levels

The majority of familial Alzheimer's disease cases have been attributed to mutations in the presenilin 1 (PS1) gene. PS1 is synthesized as an inactive holoprotein that undergoes endoproteolytic processing to generate a functional N- and C-terminal heterodimer (NTF and CTF, respectively). We identified a single residue in PS1, Ser(397), which regulates the CTF levels in a population of dimer that has a rapid turnover. This residue is part of a highly conserved glycogen synthase kinase-3beta (GSK-3beta) consensus phosphorylation site within the loop domain of PS1. Site-directed mutagenesis at the Ser(397) position increased levels of PS1 CTF but not NTF or holoprotein. Similar increases in only CTF levels were seen when cells expressing wild type PS1 were treated with lithium chloride, an inhibitor of GSK-3beta. Both wild type and PS1 S397A CTF displayed a biphasic turnover, reflecting rapidly degraded and stable populations. Rapid turnover was delayed for mutant PS1 S397A, causing increased CTF. These data demonstrate that PS1 NTF.CTF endoproteolytic fragments are generated in excess, that phosphorylation at Ser(397) by GSK-3beta regulates the discard of excess CTF, and that the disposal of surplus NTF is mediated by an independent mechanism. Overall, the results indicate that production of active NTF.CTF dimer is more complex than limited endoproteolysis of PS1 holoprotein and instead involves additional regulatory events.     

Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.

We describe here an algorithm for distinguishing sequential from nonsequentially folding proteins. Several experiments have recently suggested that most of the proteins that are synthesized in the eukaryotic cell may fold sequentially. This proposed folding mechanism in vivo is particularly advantageous to the organism. In the absence of chaperones, the probability that a sequentially folding protein will misfold is reduced significantly. The problem we address here is devising a procedure that would differentiate between the two types of folding patterns. Footprints of sequential folding may be found in structures where consecutive fragments of the chain interact with each other. In such cases, the folding complexity may be viewed as being lower. On the other hand, higher folding complexity suggests that at least a portion of the polypeptide backbone folds back upon itself to form three-dimensional (3D) interactions with noncontiguous portion(s) of the chain. Hence, we look at the mechanism of folding of the molecule via analysis of its complexity, that is, through the 3D interactions formed by contiguous segments on the polypeptide chain. To computationally splice the structure into consecutively interacting fragments, we either cut it into compact hydrophobic folding units or into a set of hypothetical, transient, highly populated, contiguous fragments ("building blocks" of the structure). In sequential folding, successive building blocks interact with each other from the amino to the carboxy terminus of the polypeptide chain. Consequently, the results of the parsing differentiate between sequentially vs. nonsequentially folded chains. The automated assessment of the folding complexity provides insight into both the likelihood of misfolding and the kinetic folding rate of the given protein. In terms of the funnel free energy landscape theory, a protein that truly follows the mechanism of sequential folding, in principle, encounters smoother free energy barriers. A simple sequentially folded protein should, therefore, be less error prone and fold faster than a protein with a complex folding pattern.     

Development of a novel liquid crystal based cell traction force transducer system

Keratinocyte traction forces play a crucial role in wound healing. The aim of this study was to develop a novel cell traction force (CTF) transducer system based on cholesteryl ester liquid crystals (LC). Keratinocytes cultured on LC induced linear and isolated deformation lines in the LC surface. As suggested by the fluorescence staining, the deformation lines appeared to correlate with the forces generated by the contraction of circumferential actin filaments which were transmitted to the LC surface via the focal adhesions. Due to the linear viscoelastic behavior of the LC, Hooke's equation was used to quantify the CTFs by associating Young's modulus of LC to the cell induced stresses and biaxial strain in forming the LC deformation. Young's modulus of the LC was profiled by using spherical indentation and determined at approximately 87.1±17.2kPa. A new technique involving cytochalasin-B treatment was used to disrupt the intracellular force generating actin fibers, and consequently the biaxial strain in the LC induced by the cells was determined. Due to the improved sensitivity and spatial resolution (～1μm) of the LC based CTF transducer, a wide range of CTFs was determined (10-120nN). These were found to be linearly proportional to the length of the deformations. The linear relationship of CTF-deformations was then applied in a bespoke CTF mapping software to estimate CTFs and to map CTF fields. The generated CTF map highlighted distinct distributions and different magnitude of CTFs were revealed for polarized and non-polarized keratinocytes.     

Force Field Bias in Protein Folding Simulations

Long timescale (>1 μs) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of sufficient simulation time. We examine one such case, the human Pin1 WW domain, using the recently developed deactivated morphing method to calculate free energy differences between misfolded and folded states. We find that the force field we used favors the misfolded states, explaining the failure of the folding simulations. Possible further applications of deactivated morphing and implications for force field development are discussed.     

Protein structure prediction using a docking-based hierarchical folding scheme

The pathways by which proteins fold into their specific native structure are still an unsolved mystery. Currently, many methods for protein structure prediction are available, and most of them tackle the problem by relying on the vast amounts of data collected from known protein structures. These methods are often not concerned with the route the protein follows to reach its final fold. This work is based on the premise that proteins fold in a hierarchical manner. We present FOBIA, an automated method for predicting a protein structure. FOBIA consists of two main stages: the first finds matches between parts of the target sequence and independently folding structural units using profile-profile comparison. The second assembles these units into a 3D structure by searching and ranking their possible orientations toward each other using a docking-based approach. We have previously reported an application of an initial version of this strategy to homology based targets. Since then we have considerably enhanced our method's abilities to allow it to address the more difficult template-based target category. This allows us to now apply FOBIA to the template-based targets of CASP8 and to show that it is both very efficient and promising. Our method can provide an alternative for template-based structure prediction, and in particular, the docking-basedranking technique presented here can be incorporated into any profile-profile comparison based method.     

When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible

One still cannot predict the 3D fold of a protein from its amino acid sequence, mainly because of errors in the energy estimates underlying the prediction. However, a recently developed theory [1] shows that having a set of homologs (i.e., the chains with equal, in despite of numerous mutations, 3D folds) one can average the potential of each interaction over the homologs and thus predict the common 3D fold of protein family even when a correct fold prediction for an individual sequence is impossible because the energies are known only approximately. This theoretical conclusion has been verified by simulation of the energy spectra of simplified models of protein chains [2], and the further investigation of these simplified models shows that their true "native" fold can be found by folding of the chain where each interaction potential is averaged over the homologs. In conclusion, the applicability of the "homolog-averaging" approach is tested by recognition of real protein 3D structures. Both the gapless threading of sequences onto the known protein folds [3] and the more practically important gapped threading (which allows to consider not only the known 3D structures, but the more or less similar to them folds as well) shows a significant increase in selectivity of the native chain fold recognition.     

An obligate intermediate along the slow folding pathway of a group II intron ribozyme

Most RNA molecules collapse rapidly and reach the native state through a pathway that contains numerous traps and unproductive intermediates. The D135 group II intron ribozyme is unusual in that it can fold slowly and directly to the native state, despite its large size and structural complexity. Here we use hydroxyl radical footprinting and native gel analysis to monitor the timescale of tertiary structure collapse and to detect the presence of obligate intermediates along the folding pathway of D135. We find that structural collapse and native folding of Domain 1 precede assembly of the entire ribozyme, indicating that D1 contains an on-pathway intermediate to folding of the D135 ribozyme. Subsequent docking of Domains 3 and 5, for which D1 provides a preorganized scaffold, appears to be very fast and independent of one another. In contrast to other RNAs, the D135 ribozyme undergoes slow tertiary collapse to a compacted state, with a rate constant that is also limited by the formation D1. These findings provide a new paradigm for RNA folding and they underscore the diversity of RNA biophysical behaviors.     

Substitution of antibodies and receptors with molecularly imprinted polymers in enzyme-linked and fluorescent assays

A new technique for coating microtitre plates with molecularly imprinted polymers (MIP), specific for low-molecular weight analytes (epinephrine, atrazine) and proteins is presented. Oxidative polymerization was performed in the presence of template; monomers: 3-aminophenylboronic acid (APBA), 3-thiopheneboronic acid (TBA) and aniline were polymerized in water and the polymers were grafted onto the polystyrene surface of the microplates. It was found that this process results in the creation of synthetic materials with antibody-like binding properties. It was shown that the MIP-coated microplates are particularly useful for assay development. The high stability of the polymers and good reproducibility of the measurements make MIP coating an attractive alternative to conventional antibodies or receptors used in enzyme linked immunosorbent assay (ELISA).     

Cooperative tertiary interaction network guides RNA folding

Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have?a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming?a unique, stable fold.