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Major increases in brightness are anticipated with the upcoming coherent X‐ray lasers. Extrapolation suggests that a single macromolecule ‘sample’ may be sufficient to generate a measurable X‐ray diffraction pattern, a continuous Fourier transform of the molecule giving easier phase determination. The practical difficulties are enormous in the recording of such diffraction patterns, not least the so‐called ‘molecule blow‐up problem’ due to the thermal and radiation blast that a single molecule must take. By taking the exposure at a sufficiently small time‐flash, a few femtoseconds, this may be practical. For 3D structure determination multiple sample orientations are needed. A risk is too few photons in the femtosecond pulse that must be used to take data before sample damage occurs. A nanocluster of molecules would be a way of compensating for that and a ‘jet stream’ of these would lead to powder diffraction patterns rather than single‐molecule patterns.

Many bioactive peptides and proteins of pharmaceutical interest are found in animal venoms. Nature often reuses scaffolds within protein frameworks to develop new properties. The binding core of the peptide from venomous animals is conserved through species (built on a small number of permissive scaffolds). The same scaffolds are often found in nature in protein, performing other non-toxic functions, and it is likely that such conserved motifs are the result of divergent evolution from a common ancestor protein framework via gene duplication. This chapter describes the use of ancestral sequence reconstruction to identify and reconstruct the evolutionary history of important physiological protein and peptide and to connect their common ancestor to certain venom peptides and proteins. This process helps with identifying which amino acids are important for functioning and which ultimately can be used to engineer new bioactive peptide with tailor made properties.

The ideal protein-expression strategy for X-ray structural analysis should provide correctly folded, soluble, and active protein in sufficient quantities for successful crystallization. Subsequent isolation and purification must be designed to achieve a polished product as rapidly as possible, involving a minimum number of steps. The simplest and least expensive methods employ bacterial hosts such as Escherichia coli, Bacillus, and Staphylococcus but if the target protein is from an eukaryotic source requiring post-translational processing for full functionality, an eukaryotic vector-host system would be appropriate. This chapter discusses the processes of cloning and expression, and protein extraction and isolation.

In the living cell, protein-DNA interactions take place during genetic processes such as chromatin organization, recombination, replication, transcription, and DNA repair. In order to fully understand the mechanism of these processes, study of protein-DNA interactions at atomic level is required. Despite the wealth of knowledge and attempts of several investigators to classify protein-DNA complexes on the basis of structural analysis of well over 200 protein-DNA complexes, the prediction and modelling based on three-dimensional structure or amino acid sequence of a protein and nucleotide sequence of DNA is challenging. X-ray crystallography is the most powerful technique used for structural studies and the development of technology for the production and purification of large quantities of proteins and DNA is vital to its success. Advances in oligonucleotide synthesis have not only provided ease of synthesis of large quantities of pure DNA but also of any required DNA sequence. This has resulted in the crystallization and structure determination of a vast number of DNA oligonucleotides and protein-DNA complexes. Since 1994 there has been a dramatic increase in the number of the protein-DNA complex structures solved annually. The first and most difficult step in the X-ray crystallographic study is the growth of well-diffracting crystals of the protein-DNA complex under investigation. This chapter describes methods employed to purify proteins and DNA for cocrystallization, procedures for crystallization of protein-DNA, and characterization of cocrystals.

This chapter explores how spin glass concepts have found use in and, in some cases, further advanced areas such as computational complexity, combinatorial optimization, neural networks, protein conformational dynamics and folding, and computer science (through the introduction of new heuristic algorithms such as simulated annealing and neural-based computation, and through new approaches to analyzing hard combinatorial optimization problems). It also introduces some “short takes” on topics that space constraints prevent covering in detail, but should be at least mentioned: prebiotic evolution, Kauffman's NK model, and the maturation of the immune response. The chapter summarizes the heart of what most people mean when they refer to spin glasses as relevant to complexity. It focuses on the early, classic papers in each subject, giving the reader a flavor of each.

This chapter examines an apparent tension created by recent research on neurological development and genetics on the one hand and cognitive development on the other. It considers what it might mean for intrinsic signals to guide the initial establishment of functional architecture. It argues that an understanding of the mechanisms by which the body develops can inform our understanding of the mechanisms by which the brain develops. It cites the view of developmental neurobiologists Fukuchi-Shimogori and Grove, that the patterning of the part of the brain responsible for our higher functions is coordinated by the same basic mechanisms and signaling protein families used to generate patterning in other embryonic organs. Thus, what's good enough for the body, is good enough for the brain.

The concept of gene pleiotropy may play a key role in developing an integrated view of protein evolution. Although the capacity of a gene that may affect multiple phenotypic characters has been used to explain many biological phenomena, little has been known about the extent of pleiotropy at the genome level. Based on the premise that links between gene pleiotropy and the dimensionality of organismal fitness, the author of this book has provided a feasible statistical framework to estimate the degree of gene pleiotropy. This chapter discusses this issue.

This chapter begins with a discussion of proteins associated with lysosomal storage diseases and their orthologues in model organisms. It then discusses studies of orthologous proteins associated with lysosomal storage diseases; biogenesis and trafficking to the lysosome; proteins associated with disease and with lysosome biogenesis and their orthologues in model organisms; and studies of orthologous proteins implicated in disease that are involved in lysosome biogenesis.

Scents play a central role in rodent societies, communicating information about identity (species, sex, individual, kinship) and status (social, reproductive, health, age). This requires the interaction between volatile and involatile molecular components of scents, the spatial deposition pattern of scent marks, and time of deposition. The major histocompatibility complex (MHC) and major urinary proteins (MUPs) are both highly polymorphic systems that contribute to scents. Most studies have focused on MHC in inbred laboratory rodents. However, studies of wild rodents are revealing that MUPs provide a species and sex-specific genetic identity signature that also underlies individual and kin recognition in house mice. MUPs are mediators of both identity and current status information. Although MHC contributes to the recognition of familiar scents, there is little evidence that it provides direct information about genetic identity.

This chapter argues that many of the human foodstuffs generated from animals have evolved at least in part as a result of reticulation. Specifically, introgressive hybridization and hybrid speciation have affected our most widely used animal protein sources such as cattle, pigs, tuna, sheep, goats, and trout as well as some of the lesser-utilized species such as peacock bass, chamois, mammoths, and partridges.

This chapter focuses on Austrian-born molecular biologist Max Perutz (1914–2002). Perutz was one of twenty scientific refugees from continental Europe who went on to win Nobel Prizes. A chemist and molecular biologist, he led the first successful attempt to discover the three-dimensional structure of protein molecules using X-ray crystallography, for which he shared the 1962 Nobel Prize. He was the founding chairman of the Laboratory of Molecular Biology in Cambridge, an institution that continues to thrive and counts thirteen Nobel Prize-winners among those who have spent time in its laboratories. Although Perutz applied to the Society for the Protection of Science and Learning (SPSL) for funding, in the event he did not need their money. His case, however, offers an excellent example of the emotional and practical support SPSL's officers extended to all academics who found themselves in precarious situations in the years following the rise to power of the Nazis in Germany and their subsequent conquest or annexation of neighbouring countries.

This chapter presents a brief overview of the molecular biology of the myelin protein genes and their expression into mRNA and protein. Topics discussed include classic myelin basic proteins and golli proteins, myelin proteolipid proteins, myelin-associated/oligodendrocyte basic protein, myelin-associated glycoprotein, oligodendrocyte-myelin glycoprotein, and peripheral myelin protein zero.

Current technologies to modify surfaces and control the surface properties are reviewed, with particular emphasis on alterations for biomedical and bioanalytical applications. A brief tutorial on the mechanisms of biomolecular adsorption provides background for understanding the relationship between surface wettability and biomolecular (particularly protein) adsorption. Methods for modifying surface wettability, materials that minimize or prevent fouling, and techniques for assessing protein fouling and the effectiveness of surface modifications are reviewed. Examples of “designer surfaces” are given, ranging from dynamic coatings in which small molecules or polymers are adsorbed on device surfaces, to covalent modifications such as PEGylation, hydrogel assembly, and the use of functionalized alkyl silanes. New device materials, including hydrogels made from PEGylated monomers, biodegradable polyesters, and photocurable perfluoropolyethers, are also discussed. The chapter closes with approaches that lead to the direct and indirect capture of proteins and peptides and the integration of live cells with microfluidic devices.

The perspective on natural history and medicine by Emile Zuckerkandl combined with the chemical expertise of Linus Pauling generated many novel ideas concerning molecular evolution. These included generating multiple sequence alignments, determining phylogenetic relationships based on sequence data, formulating the molecular clock hypothesis, and the proposal to resurrect ancestral sequences based on information contained within extant sequences, inter alia. Although the field of ancestral sequence reconstruction is still burgeoning, the concepts guiding the field are embraced by today's community more so than when originally proposed by Zuckerkandl and Pauling. This chapter presents a view of the field of ancestral sequence reconstruction, including recognition that genes are dynamic fossils in that they record ancient events while still adapting to new environments. It concludes with a discussion of the potential of combining ancestral sequence space and synthetic biology to expand protein functionality for directed evolution studies.

Modeling of sequence evolution is fundamental to ancestral sequence reconstruction. Care must be taken in choosing a model, however, as the use of unrealistic models can lead to erroneous conclusions. The choice of model and the effects of assumptions inherent within are discussed in this chapter in terms of their effects on probabilistic ancestral sequence reconstruction. This chapter discusses standard probabilistic models, site rate variation to these models, and deviations from the standard (homogeneous, stationary, reversible) models. Model selection, selecting one model from many, given data, and the comparison of different models are included as well as covarion models, the use of outside information when modeling, and the treatment of gaps.