Colloquia

In order for our body to heal and repair injury, cell sheets must move together to seal a gap. To overcome infection, white blood cells need to track down and destroy pathogens. Such processes can only work if cells can "sense" their environment and "decide" to move in the right direction, or else, to coordinate with neighbouring cells. This requires tight control of adhesion between cells, as well as the speed and direction of cell migration. In this talk, I will describe mathematical and computational research on cell migration, both in normal and abnormal (cancer) cells. I will focus mainly on recent "multi-scale" modeling, where we combine our understanding of the "molecular machinery" inside cells, with information about how cells interact with one another. We use this approach to investigate the behaviour of groups of cells. Combining mathematics and computational methods, we can get some insights on cell organization in development and in wound healing, as well as what could go wrong in disease such as cancer.

Protein is matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with diverse biochemistry. But it is also a point along an evolutionary trajectory determined by the protein’s function within a hierarchy of interwoven interaction networks of the cell, the organism, and the population. Thus, a theory of proteins needs to unify both aspects, the biophysical and the evolutionary. In this talk, a physical approach to the protein problem will be described, focusing on how cooperative interactions among the amino acids shape the evolution of the protein. This view of protein as evolvable matter will be used to examine basic questions about its fitness landscape and gene-to-function map.

This talk has three parts. The first part is an introduction to Hamilton’s two monumental papers from 1834-1835, which introduced the Hamilton-Jacobi equation, Hamilton’s equations of motion and the principle of least action. These three formulations of classical mechanics became the three forerunners of quantum mechanics; but ironically none of them is what Hamilton was looking for -- he was looking for a “magical” function, the principal function S(q_1,q_2,t) from which the entire trajectory history can be obtained just by differentiation (no integration). In the second part of the talk I argue that Hamilton’s principal function is almost certainly more magical than even Hamilton realized. Astonishingly, all of the above formulations of classical mechanics can be derived just from assuming that S(q_1,q_2,t) is additive, with no input of physics. The third part of the talk will present a new formulation of quantum mechanics in which the Hamilton-Jacobi equation is extended to complex-valued trajectories, allowing the treatment of classically allowed processes, classically forbidden process and arbitrary time-dependent external fields within a single, coherent framework. The approach is illustrated for barrier tunneling, wavepacket revivals, nonadiabatic dynamics, optical excitation using shaped laser pulses and high harmonic generation with strong field attosecond pulses.

The structural complexity of composite biomaterials and biomineralized particles arises from the hierarchical ordering of inorganic building blocks over multiple scales. While empirical observations of complex nanoassemblies are abundant, physicochemical mechanisms leading to their geometrical complexity are still puzzling, especially for non-uniformly sized components. These mechanisms are discussed in this talk taking an example of hierarchically organized particles with twisted spikes and other morphologies from polydisperse Au-Cys nanoplatelets [1]. The complexity of these supraparticles is higher than biological counterparts or other complex particles as enumerated by graph theory (GT). Complexity Index (CI) and other GT parameters are applied to a variety of different nanoscale materials to assess their structural organization. As the result of this analysis, we determined that intricate organization Au-Cys supraparticles emerges from competing chirality-dependent assembly restrictions that render assembly pathways primarily dependent on nanoparticle symmetry rather than size. These findings open a pathway to a large family of colloids with complex architectures and unusual chiroptical and chemical properties. The GT-based design principles for complex chiral nanoassemblies are extended to engineer drug discovery platforms for Alzheimer syndrome [3], materials for chiral photonics, vaccines, and antivirals. Developed GT methods were applied to the design of complex biomimetic composites for energy and robotics applications [2,4] will be shown as a nucleus for discussions. References [1] W. Jiang, Z.-B. et al, Emergence of Complexity in Hierarchically Organized Chiral Particles, Science, 2020, 368, 6491, 642-648. [2] Wang, M.; Vecchio, D.; et al Biomorphic Structural Batteries for Robotics. Sci. Robot. 2020, 5 (45), eaba1912. https://doi.org/10.1126/scirobotics.aba1912. [3] Jun Lu, et al, Enhanced optical asymmetry in supramolecular chiroplasmonic assemblies with long-range order, Science, 2021, 371, 6536, 1368 [4] D. Vecchio et al, Structural Analysis of Nanoscale Network Materials Using Graph Theory, ACS Nano 2021, 15, 8, 12847–12859.

A wide variety of chemical transformations can be induced by the application of force or stress to reactive systems. In some cases, these reactions are undesired, including some tribochemical (friction-induced) reactions and bond-breaking in polymers under stress. A large and growing set of examples shows that mechanochemistry can be harnessed for useful chemical transformations, making the case for mechanochemistry as a general-purpose tool to advance chemical innovation. In order to realize this vision, we require greater understanding of how force and stress can be focused on particular bonds and reaction coordinates, and how this enhances chemical reactivity and selectivity. In this talk, I will outline strategies for applying stress to quantum-mechanical models of reactive chemical systems and for understanding the resulting mechanochemical reaction pathways. I will also describe the development of interatomic potential models that can enable larger-scale models of mechanochemical and piezoelectric effects in molecules, 2D materials, and polar solids.

Controlling the properties of chemical bonds by an external stimulus is a central goal in chemistry. At the level of individual bonds, such control was achieved using light, current, electrochemical potential and electric field. In my talk, I will show that the size and direction of applied magnetic fields can affect bond stability, interatomic distance, and bond-formation probability. This behavior is demonstrated in a variety of atomic wires and single-molecule junctions. The revealed magneto-structural phenomena show that the influence of magnetic interactions on chemical bonds can be dramatic in nanoscale systems.

Until very recently, the accuracy of protein-design calculations was considered too low to enable the design of large proteins of complex fold. As a result, enzyme and binder optimization has relied on random or semi-rational mutagenesis and high-throughput screening. Our lab is developing a unique approach that combines structural bioinformatics analyses with atomistic design calculations to dramatically increase the accuracy of design calculations. Using this strategy, we have developed several general and completely automated methods for optimizing protein stability and activity. I will briefly discuss the fundamentals of this strategy and show case studies of large and complex proteins that we and our collaborators have optimized. Our lab’s long-term and still-unmet research goal is to enable the completely automated design of any biomolecular activity, and I will focus on our current research directions including the design of new enzymes and binders.

Proteins, which are at the heart of many biological processes, are involved in a variety of self-assembly processes that are controlled by various chemical and physical interactions. Quantifying the driving forces that govern these processes and particularly the trade-offs between them is essential to obtaining a more complete understanding of protein dynamics and function. In my lecture, I will discuss the molecular determinants that govern linear diffusion of proteins along DNA or along microtubules. These and other cellular processes, such as protein folding, are subject to conflicting forces some of which are regulated by post-translational modifications. Understanding the trade-offs between the stability, affinity and mobility is not only essential to decipher transport processes in the cell but also for formulating concepts for their engineering. I will discuss the power of computational models in formulating fundamental biomolecular concepts and in predicting novel principles of cellular function or for its optimization.

Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging approach is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In my talk I will discuss the information that can be retrieved by such experiments as well as the applicability of the method by presenting the characterization of engineered proteins, drug binding, antibody specificity and protein-protein interactions.

Understanding how order evolves during crystallization represents a long-standing challenge. We will describe our recent studies on crystallization of organic molecules and proteins by cryo-TEM imaging and cryo-STEM tomography. They reveal mechanisms, in which order evolution proceeds via diverse pathways, including various intermediate states. Based on these findings, we suggest a general outlook on molecular crystallization.

We study the assembly of programmable quasi-2D DNA compartments as “artificial cells” from the individual cellular level to multicellular communication. We will describe recent progress toward autonomous synthesis and assembly of cellular machines, synchrony, pattern formation, fuzzy decision-making, memory transactions, and electric field manipulation of gene expression.

Colloidal semiconductor nanocrystals have turned over the past three decades from a scientific curiosity to a component in numerous commercial products, particularly in displays, lighting and light detection. On the one hand these are complex chemically synthesized entities, and on the other they behave, in many senses, as ‘giant’ artificial atoms. The interplay between these two enables us to imbue them with unique optical properties by design of their internal structure. I will go over some of our recent efforts in utilizing designer nanocrystals for various applications, including luminescence upconversion (the conversion of two low energy photons into a single high energy photon), electric field sensing and optical gain. Finally, I will discuss opportunities for the development of colloidal sources of non-classical states of light and our recent advances in quantum spectroscopy, enabling to study the optical and electronic properties of single quantum dots with unprecedented precision.

The size, structural complexity, and functional perfection of proteins, raise a question for which we so far have no answer: How did the very first protein(s) evolve? Protein synthesis depends on dozens of highly sophisticated proteins thus presenting a chicken-egg dilemma. The most common explanation is that proteins emerged from short and simple polypeptides, that further expanded in length and complexity to give proteins as we know them today. Can we reconstruct such early polypeptide ancestors? Can a short polypeptide confer biochemical functions that are reminiscent of modern proteins? And can such polypeptides be evolutionary linked to their modern descents? I will discuss our most recent findings with respect to the polypeptide precursors of nucleotide binding proteins, and the emergence of the first cationic amino acid.

Living cells regulate their volume using a diverse set of mechanisms, to maintain their structural and functional integrity. The most widely-used mechanism to control cell volume is active ion transport. Experiments on adhered cells surprisingly revealed that their volume is significantly reduced as their basal area is increased1. We have developed a physical theory2 which considers both electrostatics and cell activity to predict a generic relation for how adhered cells regulate their volume in response to changes in their area, in agreement with the observations. Those measurements also show that the nuclear volume scales with the cell volume. Recently, the Volk group3 using intact-organism imaging, discovered that changes in nuclear volume dramatically varies the spatial organization of chromatin (DNA and associated proteins); this may have important consequences for gene expression. A simple polymeric model4 that includes the competition of chromatin self-attraction and interactions with the nuclear membrane, predicts transitions in the chromatin organization relative to the nucleus from peripheral to central to conventional, as the nuclear volume is reduced, as measured in the experiments of the Volk group.

Respiratory viruses such as coronavirus spread from person to person through droplets of saliva or mucus. Face masks decrease the dissemination of such droplets and thereby minimize viral propagation from someone who may be contagious. Mucus did not evolve, though, to help pathogens spread. Quite the opposite. Mucus arose early in the evolution of multicellular animals to exclude undesirable bacteria from body tissues, a primitive type of immunity. The cooperation between cilia* and mucus also helped prevent aquatic organisms from being smothered by sediments and enabled them to clean or collect particulate matter from their exteriors. Producing mucus was likely a prerequisite for evolution of the gut and of the types of respiratory organs necessary for terrestrial life. Today, mucus protects the large, exposed interior surfaces of our respiratory and gastrointestinal tracts from bacteria, viruses, parasites, and chemical/physical hazards. But what material is mucus? Mucus is a hydrogel made of heavily glycosylated protein molecules called “mucins,” each of which is nearly 3 megadaltons in size. Individual giant mucin molecules are disulfide bonded to one another, generating an extended mesh. Using cryo-electron microscopy and X-ray crystallography, we have discovered the three-dimensional structure of mucins and gained insight into the mechanism by which they assemble step-wise into hydrogels. ______________________________________________________ * cell-surface, rope-like structures that beat in coordinated waves

Characterization of the overall topology and inter-subunit contacts of protein complexes, and their assembly/disassembly and unfolding pathways, is critical because protein complexes regulate key biological processes, including processes important in understanding and controlling disease. Tools to address structural biology problems continue to improve. Native mass spectrometry (nMS) and associated technologies such as ion mobility are becoming an increasingly important component of the structural biology toolbox. When the mass spectrometry approach is used early or mid-course in a structural characterization project, it can provide answers quickly using small sample amounts and samples that are not fully purified. Integration of sample preparation/purification with effective dissociation methods (e.g., surface-induced dissociation), ion mobility, and computational approaches provide a MS workflow that can be enabling in biochemical, synthetic biology, and systems biology approaches. Native MS can determine whether the complex of interest exists in a single or in multiple oligomeric states and can provide characterization of topology/intersubunit connectivity, and other structural features. Beyond its strengths as a stand-alone tool, nMS can also guide and/or be integrated with other structural biology approaches such as NMR, X-ray crystallography, and cryoEM.

Arid and semi-arid regions belong to the most vulnerable climate change “hot spots” while also contributing to global scale variations in the carbon and water cycles. In particular, this is because of their high sensitivity to changes in precipitation and surface energy budgets and to the large changes in land-use taking place in these regions. This requires improving the representation of these ecosystems in land surface and ecosystem models. Improving observational approaches is also required to assess variations in their water carbon and energy exchange and to identify underlying processes. The more exotic observational sites, such as those at the semi-arid ‘timber-line’, do not always fit the large-scale patterns, but provide important test beds for predicted changes in ecosystem functioning. I will review a few examples from the Yatir site operating at the edge of the Negev desert for past 20 years, to demonstrate distinctive ecosystem response to environmental conditions and its implications.

Decoding during ribosomal translation occurs through complex and interdependent molecular recognition networks between mRNA, tRNA, and rRNA. Among those, the stability of codon-anticodon triplets, the fold of the tRNA anticodon hairpin, the modified nucleotides, and the interactions with rRNA bases at the decoding site cosntitute key contributors. On the basis of biochemical and genetic data in the literature, coupled with many crystal structures of fully active ribosomes, nucleotide modifications at positions 34 and 37 of the anticodon loop are now understood molecularly. Both pre-organize the anticodon loop for efficient mRNA binding. The modifications at 37 stabilize AU-rich codon-anticodon pairs and maintain the coding frame. The modifications at 34 help to avoid miscoding and allow to decode purine-ending codons in split codon boxes by promoting base pairing that can be accommodated within the structural constraints of the ribosomal grip at the decoding site. Depending on the codon box, the tRNA modifications allow for diversity in codon usage depending on genomic GC content as well as on the number and types of isoacceptor tRNAs. Although universal, the genetic code is not translated identically and differences exist not only between organisms in the three kingdoms of life but also between cellular types. To decipher diversely but efficiently the genetic code, cells developed sophisticated arrays between tRNA pools and tRNA modifications, anchored in the cellular metabolic enzymatic pathways and guaranteeing protein homeostasis. Examples of mutations leading to specific human diseases in some of those enzymes will be described.

In this symposium, I will introduce our recent results how to construct dynamic self-assembled nanostructures exhibiting switchable functions, inspired by life systems. For example, synthetic tubular pores are able to undergo open-closed gating driven by an external signal, which function as an artificial enzyme. When self-assembled tubules embed DNA inside the hollow cavities, the DNA-coat assembly undergoes collective motion in helicity switching. In the case of toroid assembly, the static toroids are able to undergo spontaneous helical growth when they switch into out-of-equilibrium state. The helical growing drives actuation of spherical vesicles into tubular vesicles, reminiscent of microtubles. Moving from 1-D to 2-D structures, the internal pores are able to form chiral interior which selectively capture only one enantiomer in racemic solution with pumping action. I will discuss recently discovered these results with their complex functions.

Protein design—i.e., the construction of entirely new protein sequences that fold into prescribed structures—has come of age: it is possible now to generate a wide variety stable protein folds from scratch using rational and/or computational approaches. A challenge for the field is to move from what have been largely in vitro exercises to protein design in living cells and, in so doing, to augment biology. This talk will illustrate what is currently possible in this nascent field using de novo -helical coiled-coil peptides as building blocks.1 Coiled coils are bundles of 2 or more  helices that wrap around each other to form rope-like structures. They are one of the dominant structures that direct natural protein-protein interactions. Our understanding of coiled coils provides a strong basis for building new proteins from the bottom up. The first part of this talk will survey this understanding,1 our design methods,2,3 and our current “toolkit” of de novo coiled coils.4-6 Next, I will describe how the toolkit can be used to direct protein-protein interactions and build complex protein assemblies in bacterial cells. First, in collaboration with the Savery lab (Bristol), we have used homo- and hetero-oligomeric coiled coils as modules in engineered and de novo transcriptional activators and repressors.7 Secondly, with the Warren (Kent) and the Verkade (Bristol) labs, we have engineered hybrids of a de novo heterodimer and a natural component of bacterial microcompartments to form a “cytoscaffold” that permeates E. coli cells.8 This can be used to support the co-localisation of functional enzymes.