Hongbin Li

Hydrogels are water-containing soft materials made of cross-linked polymer networks. Hydrogels can emulate many features of native tissues and organisms, and have therefore found many applications in biomedical studies. Recently, driven by the needs for stimuli-responsive materials in various biomedical applications, “dynamic” hydrogels that can change their physical, chemical, biological, or mechanical properties have attracted increasing interest. Recombinant proteins are promising hydrogel building blocks due to their biocompatibility, diverse biofunctions, and designable structures. Moreover, stimuli-responsive conformational changes and interactions of proteins provide possibilities for constructing dynamic protein-based hydrogels.This thesis reviews the state-of-the-art studies of dynamic protein-based hydrogels, including the cross-linking methods, the design principles, and the future directions of this field. Driven by the needs for more predictable, sensitive, and reversible hydrogels, we engineer novel protein-based hydrogels in this thesis. An elastomeric protein-based hydrogel is first engineered with thermo-responsive properties, which is controlled by the thermo-responsive in situ phase transition of the polypeptide side chains in the hydrogel network. Then, two dynamic hydrogels are physically cross-linked by a coiled coil interaction and a protein-protein interaction, respectively, which both exhibit time-dependent viscoelastic properties, multiple energy dissipation modes, and injectability. The viscoelastic properties of these two physically cross-linked hydrogels are stimuli-responsive due to the stimuli-responsive nature of their cross-linking methods. Finally, a light-controlled information writing approach is developed by using a light-responsive protein-protein interaction to decorate fluorescent proteins onto protein-based hydrogel blank slates. Consequently, 2D/3D fluorescence images can be produced and stored in protein-based hydrogels.The developed hydrogels are mainly responsive to temperature or light, which are two types of stimuli that have been widely adapted as therapeutic tools in biomedical studies. The stimuli-responsive property changes in the developed hydrogel systems are highly dose-sensitive and reversible, which facilitates customized fine tuning of hydrogel functionality. Therefore, we anticipate that these developed dynamic protein-based hydrogels will find various applications in biomedical studies. Moreover, the results of this thesis are expected to contribute to the quantitative prediction of dynamic hydrogel properties and inspire the bottom-up designs of other dynamic hydrogels.

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Metalloproteins account for more than one-third of all proteins in nature and play important roles in biological processes. The folding process of metalloproteins is complicated, as it is driven by not only the polypeptide chain folding effect but also the metal coordination. Folding into the native structures with correctly assembled metal cofactors is a prerequisite for metalloproteins to perform their biological functions. Therefore, understanding the folding-unfolding mechanisms of metalloproteins is of critical importance. Over the past two decades, single-molecule force spectroscopy (SMFS) has evolved into a powerful method to investigate the folding-unfolding mechanisms of metalloproteins at the single-molecule level. This thesis presents the SMFS studies on the folding-unfolding mechanisms of four important metalloproteins, including three iron-sulfur proteins and one heme-containing protein. First, we studied the mechanical unfolding behavior of a high potential iron-sulfur protein by atomic force microscopy (AFM)-based SMFS, and revealed a detailed mechanical unfolding mechanism. In combination with previous studies, we proposed a general mechanical unfolding mechanism for the iron-sulfur protein family. We then investigated the folding behavior of the simplest iron-sulfur protein, rubredoxin, with optical tweezers (OT)-based SMFS. We discovered a novel binding-folding-reconstitution mechanism of the folding of rubredoxin, and highlighted the critical importance of the two-coordinate ferric site in the folding of rubredoxin. We also explored the folding behavior of another iron-sulfur protein, ferredoxin, with OT-based SMFS. The unfolded ferredoxin was found to mostly misfold instead of folding back to its native structure; however, the successful reconstitution of the β-sheet or the coordination center was observed in rare cases. In addition, we studied the folding-unfolding behavior of a heme-containing protein, cytochrome c, using OT-based SMFS. We revealed a detailed folding-unfolding mechanism for holo-form cytochrome c, and identified the deviation from random coil behavior of apo-form cytochrome c, which was previously inaccessible by ensemble spectroscopic studies. Finally, conclusions and future directions on investigating the folding-unfolding mechanisms of metalloproteins with SMFS were presented. Overall, this thesis advances our understanding of the folding-unfolding mechanisms of iron-sulfur proteins, heme-containing proteins, as well as metalloproteins in general, and the systematic studies pave the way for further research in this important area.

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Most recently, hydrogels composed of recombinant proteins/peptides have attracted great interest due to their diverse biofunctions, designable amino acids sequence, reactive side chains, excellent biocompatibility and biodegradability. Moreover, conformational switching of folded proteins induces structural and thermodynamic changes in the network, leading to dynamic properties and energy dissipative ability of hydrogels. Despite these advantages, applications of recombinant protein-based hydrogels are often limited by their poor mechanical performance and inefficient network crosslinking, due to steric hindrance of bulky protein domains in the networks. To optimize mechanical behaviors of structural protein-based hydrogels, it is important to understand the design principles of globular protein-based elastomeric networks. This thesis discusses the latest research on protein-based hydrogels, including network designs, crosslinking strategies, and resulting physical and mechanical features of the materials. In addition, classic rubber elasticity theory is introduced to reveal the effects of elastomeric network on physical and mechanical properties of synthetic polymer hydrogels. Based on the theory, a semi-quantitative tool was developed to predict/explain mechanical properties of globular folded polyprotein-based hydrogels, providing guidance for the rational design of globular polyprotein-based hydrogels with desired mechanical properties. Furthermore, we demonstrate for the first time that the macroscopic mechanical energy generated from conformational change of globular proteins closely corresponds to single molecule mechanochemical events by investigating mechanochemical coupling cycles of globular folded proteins at both single-molecule and macroscopic levels.With the guidance of the design principle, we describe synthesis of super tough protein-based hydrogels based on a novel denatured-crosslinking hydrogelation method, which provides potential cartilage-like biomaterials and a general strategy for mechanical enhancement for protein-based hydrogels. We also explored the synthesis of super tough protein-alginate hybrid hydrogels using a double-network approach, further broadening the range of mechanical properties that protein-based biomaterials can reach. Taking advantage of precise mechanical control and dynamic behaviors of mutually exclusive protein-based hydrogels, an application of protein-based hydrogels is reported as extracellular matrices for cell spreading studies, demonstrating a great potential utility of dynamic protein hydrogels in cellular mechano-biology studies.

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Understanding the molecular mechanism of protein folding has always remained a challenging problem. Extensive investigations based on ensemble methods have been carried out to shed light on the protein folding problem. Compared with ensemble-averaged measurements, single-molecule force spectroscopy (SMFS) has evolved as a powerful technique to probe mechanical unfolding/folding of proteins at the single-molecule level, which provides rich details of protein conformational changes. Optical tweezers (OT), as one representative SMFS technique, have been widely used to directly monitor a protein folding process. This thesis presents a series of studies that use OT to investigate the mechanical unfolding/folding of two distinct classes of proteins: knotted/slipknotted proteins and Ca²⁺-binding metalloproteins.First, we combined OT and steered molecular dynamics (SMD) simulations to investigate a complex slipknotted protein. When stretched from the N- and C-termini, the slipknotted structure could be completely untied via multiple unfolding pathways. Upon relaxation, this protein showed complex folding behaviors involving misfolding. Our studies demonstrate the unfolding/folding mechanisms of a slipknotted protein with a complex topological conformation.Second, we used OT to mechanically tighten, untie and retie a trefoil knotted protein. Our results revealed that protein folding with a preformed knot was fast and robust; however, the folding from the unfolded polypeptide chain without the knot conformation was significantly slower, suggesting that the knotting was the rate-limiting step for the folding of this trefoil knotted protein.Next, we investigated the mechanical unfolding/folding behaviors of a Ca²⁺-binding protein, RTX (repeats-in-toxin) block V. Our results elucidated the secretion mechanism of this RTX block V and revealed that the mechanical design can ensure an efficient translocation process.Finally, we used OT to study another Ca²⁺-binding protein, RTX block IV. The mechanical properties of RTX block IV was well-characterized. Our results revealed that RTX block IV follows a similar translocation mechanism to be secreted as RTX block V. We also suggested that the secreted RTX block V is stabilized by folded RTX block IV and protected from being unfolded in vivo.Overall, this thesis clarified the unfolding/folding mechanisms of two knotted/slipknotted proteins and Ca²⁺-binding protein RTX.

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Hydrogels are crosslinked polymer networks that absorb large amounts of aqueous solutions. The varieties of hydrogel building blocks include natural polymers, synthetic polymers and genetically engineered proteins. This dissertation will discuss the latest progress of hydrogels constructed from genetically engineered proteins (recombinant proteins), mainly focusing on biorecognition-driven physical hydrogels as well as chemically crosslinked hydrogels. Examples include dynamic hydrogels and designing hydrogels via protein fragments reconstitution.The first class of studies presented in this dissertation involves the use of molecular level processes to control macroscopic mechanical properties. A novel protein hydrogel is reported showing dynamic mechanical properties based on a redox potential controlled protein folding-unfolding switch, which is constructed from a designed mutually exclusive protein. The changes of the mechanical and physical properties of this hydrogel are fully reversible and can be applied as extracellular matrix to investigate cell response upon varying stiffness. In addition, another powerful method, metal chelation, is reported to tune the conformational change of mutually exclusive protein, which can stabilize the domain, initiate the folding switch and further affect the mechanical properties of resultant hydrogel.In the second class of studies, protein fragment reconstitution has been demonstrated as a novel driving force for engineering self-assembling reversible protein hydrogels. Protein fragment reconstitution, also known as fragment complementation, is a self-assembling mechanism by which protein fragments can reconstitute the folded conformation of the native protein when split into two halves. GL5 is a small peotein, which is capable of fragment reconstitution spontaneously when split into two halves, GN and GC. Using GL5 as a model, different building blocks are designed to engineer self-assembling, physically crosslinked protein hydrogels. These novel hydrogels show temperature-dependent reversible sol-gel transition, and excellent property against erosion in water. It is anticipated that such fragment reconstitution may offer a general driving force for engineering protein hydrogels from a variety of proteins, expanding the horizon of “bottom-up” approaches in the design principles of biomaterials.

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The knotted polypeptide chain is one of the most surprising topological features found in certain proteins. Understanding how knotted proteins overcome the topological difficulty during the folding process has become a challenging problem. Theoretical studies suggest that a slipknotted structure can serve as an important intermediate in the transformation from unknotted structure to a knotted structure. This thesis mainly focuses on the mechanical folding/unfolding of a slipknotted protein, the ORF109 of the Acidianus Filamentous Virus 3 (AFV3-109), using single-molecule force spectroscopy (SMFS). To show the power of atomic force microscopy (AFM) in the study of SMFS, an α/β protein, NuG2, is stretched and relaxed at a single-molecule level using AFM and the mechanical unfolding and folding events are directly observed. By applying force onto AFV3-109 in different directions, we are able to untie the slipknot to a linear polypeptide chain, as well as tighten it into a trefoil knot involving ∼ 13 amino acid residues. Multiple pathways of untying and tightening are found by both SMFS experiments and Steered Molecular Dynamics (SMD) simulations, revealing that the kinetic partitioning mechanism governs the unfolding of the slipknotted protein. In addition, SMD simulations provide detailed molecular mechanisms of the unfolding of the protein and the topological changes from a slipknot to a linear chain, as well as from a slipknot to a trefoil knot. Moreover, the mechanical folding of AFV3-109 is directly observed using optical tweezers, providing new insight into the folding mechanism of knotted/slipknotted proteins.

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The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.

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New generations of protein-based hydrogels are being developed rapidly over the last several decades for potential applications in biomedicine as well as basic biological studies. Protein-based hydrogels have been explored as synthetic extracellular matrices (ECM) for applications in cell culture and tissue regeneration. A variety of proteins, including silk protein, fibrin, collagen and elastin have been studied. Most of these proteins are non-globular proteins. However, a large number of ECM proteins are tandem modular proteins that consist of many individually folded domains. We hypothesize that tandem modular proteins may also be used in constructing novel hydrogels that can mimic the physical and biochemical characteristics of natural extracellular matrices. In this dissertation, we explored the feasibility of using tandem modular proteins for constructing protein-based biomaterials.First, through self-assembly of two complementary leucine zipper sequences, artificial tandem modular proteins were engineered to form physically cross-linked hydrogels mimicking ECM.Going a step further, a photochemical cross-linking strategy is employed to covalently cross-link engineered artificial elastomeric protein to biomaterials that exhibit mechanical properties mimicking the passive elasticity of muscles. To optimize the biocompatibility of the tandem modular protein-based hydrogels, a protein domain which contains cell-binding sequences is used to construct ECM-mimetic hydrogels. The hydrogels can support cell adhension. Our result also suggests a possible method to design functional hydrogels.To prove the possibility of designing functional hydrogels, an xylanase was used to design enzymatic hydrogels. Our result shows that the enzymes remain active after being cross-linked into hydrogels.The possibility was further proved by fluorescent hydrogels designed from tandem modular protein based on Cyan Fluorescent Protein (CFP) and Yellow Fluorescent Protein (YFP). The fluorescent hydrogels can be applied as force sensors in cells with picoNewton (pN) sensitivity.

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The mechanical folding/unfolding of proteins is involved in many biological processes. However, the molecular mechanism underlining the mechanical folding/unfolding of proteins remains an open question. Most of the current knowledge about the protein folding is from ensemble measurements. In the study of the molecular mechanism underlying the mechanical folding/unfolding of proteins, single molecule atomic force microscopy (AFM) has its unique advantages. Although many endeavors have been made by using single molecule AFM to study the mechanical folding/unfolding of proteins and numerous interesting details have been revealed, the underlying mechanism of protein mechanical folding/unfolding remains largely unknown. The main objective of this thesis is to study the mechanical folding/unfolding of some model proteins using single molecule AFM. First, we studied the mechanical unfolding pathways of two domain-insertion proteins: a natural one, T4-lysozyme (T4L), and an artificially designed one, GL5/T4L (GL5: a mutant of protein GB1). Our study on T4L provided the first direct evidence of the kinetic partitioning assumption for protein folding at the single molecule level. Our study on GL5/T4L revealed its mechanical unfolding pathway with a reversed mechanical unfolding hierarchy. The designing ofdomain-insertion proteins also presented a new concept to program the mechanical unfolding pathway of multi-domain proteins. Second, we studied the mechanical folding/unfolding of TNfn3 domain by combining single molecule AFM with the steered molecular dynamics (SMD) simulation and protein engineering. The mechanical design of TNfn3 was found robust and thebackbone H-bonds of TNfn3 were found critical for its mechanical stability. Our results showed the first direct evidence that the mechanical folding pathways of TNfn3 aregoverned by kinetic partitioning. Third, we studied the folding/unfolding kinetics and mechanics of an artificially designed mutually exclusive protein GL5/I27w34f (I27w34f: a tryptophan removed mutant of I27). The mutually exclusive protein GL5/I27w34f is designed to mimic the natural domain-insertion proteins which are typically difficult to study directly. Our study provided the first direct evidence that protein folding can generate sufficient mechanical strain to unravel a host protein and the folding of mutually exclusive proteins involving a tug-of-war. Mutually exclusive proteins provide a new system for manipulating proteinfolding.

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Elastomeric proteins are an important class of mechanical proteins that take care of the strength, elasticity and extensibility of tissues and biological machineries. Elastomeric proteins are also essential building blocks of materials with outstanding mechanical properties. However, it was largely unknown how elastomeric proteins achieve the remarkable mechanical stability until the advent of single molecule force spectroscopy techniques, such as single molecule atomic force microscopy (AFM). Single molecule AFM has enabled the direct characterization of the mechanical properties of elastomeric proteins at the single molecule level and led to the new promising research area of single protein mechanics and engineering. Combined with molecular dynamics simulation and protein engineering, single molecule AFM has provided rich information about the mechanical design of elastomeric proteins. This dissertation focuses on engineering proteins with novel mechanical properties and makes use of this new technique. It is demonstrated how a non-mechanical protein GB1, the B1 immunoglobulin (IgG) binding domain of protein G from Streptococcus, shows superb mechanical stability. We also investigated the effect of denaturant, guanidium hydrochloride (GdmCl), on the mechanical stability of GB1. It was found that the mechanical stability of GB1 decreases with the increase of GdmCl concentration. Using GB1 as a model system, we demonstrated two ways to enhance the mechanical stability of proteins: by metal chelation and by stabilizing protein-protein interactions. It is revealed that preferentially stabilizing the native state over the mechanical unfolding transition state of proteins is the key to achieve enhanced mechanical stability. We also showed two applications of engineered elastomeric proteins. One is the design of an artificial elastomeric protein with dual mechanical stability that can be regulated reversibly by protein-protein interactions. We introduced proline mutations to GB1 to make it mechanically labile and behave as entropic springs. Upon binding of the Fc fragment of IgG, the proline mutants of GB1 switched into a state of significant mechanical stability and can serve as shock-absorbers. The other application is the engineering of the first tandem modular protein based thermo-reversible hydrogel, which paves the way for engineering hydrogels with much improved physical properties that can be used as artificial extracellular matrices and tissue engineering materials.

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