Collagen is the main structural protein in the extracellular matrix of a body's various connective tissues. As the main component of connective tissue, it is the most abundant protein in mammals. 25% to 35% of a mammalian body's protein content is collagen. Amino acids are bound together to form a triple helix of elongated fibril known as a collagen helix. The collagen helix is mostly found in connective tissue such as cartilage, bones, tendons, ligaments, and skin. Vitamin C is vital for collagen synthesis, while Vitamin E improves its production.
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.
(2S,4R)-4-Hydroxyproline, or L-hydroxyproline (C5H9O3N), is an amino acid, abbreviated as Hyp or O, e.g., in Protein Data Bank.
In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system on the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.
A polyproline helix is a type of protein secondary structure which occurs in proteins comprising repeating proline residues. A left-handed polyproline II helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have trans isomers of their peptide bonds. This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. Similarly, a more compact right-handed polyproline I helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly and have cis isomers of their peptide bonds. Of the twenty common naturally occurring amino acids, only proline is likely to adopt the cis isomer of the peptide bond, specifically the X-Pro peptide bond; steric and electronic factors heavily favor the trans isomer in most other peptide bonds. However, peptide bonds that replace proline with another N-substituted amino acid are also likely to adopt the cis isomer.
Cyclic peptides are polypeptide chains which contain a circular sequence of bonds. This can be through a connection between the amino and carboxyl ends of the peptide, for example in cyclosporin; a connection between the amino end and a side chain, for example in bacitracin; the carboxyl end and a side chain, for example in colistin; or two side chains or more complicated arrangements, for example in alpha-amanitin. Many cyclic peptides have been discovered in nature and many others have been synthesized in the laboratory. Their length ranges from just two amino acid residues to hundreds. In nature they are frequently antimicrobial or toxic; in medicine they have various applications, for example as antibiotics and immunosuppressive agents. Thin-Layer Chromatography (TLC) is a convenient method to detect cyclic peptides in crude extract from bio-mass.
Ronald T. Raines is an American chemical biologist. He is the Roger and Georges Firmenich Professor of Natural Products Chemistry at the Massachusetts Institute of Technology. He is known for using ideas and methods of physical organic chemistry to solve important problems in biology.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.
Melanocortin 3 receptor (MC3R) is a protein that in humans is encoded by the MC3R gene.
Radical SAM enzymes belong to a superfamily of enzymes that use an iron-sulfur cluster (4Fe-4S) to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical (5'-dAdo), as a critical intermediate. These enzymes utilize this radical intermediate to perform diverse transformations, often to functionalize unactivated C-H bonds. Radical SAM enzymes are involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC. Radical SAM enzymes comprise the largest superfamily of metal-containing enzymes.
A stapled peptide is a modified peptide, typically in an alpha-helical conformation, that is constrained by a synthetic brace ("staple"). The staple is formed by a covalent linkage between two amino acid side-chains, forming a peptide macrocycle. Staples, generally speaking, refer to a covalent linkage of two previously independent entities. Peptides with multiple, tandem staples are sometimes referred to as stitched peptides. Among other applications, peptide stapling is notably used to enhance the pharmacologic performance of peptides.
Ancient proteins are complex mixtures and the term palaeoproteomics is used to characterise the study of proteomes in the past. Ancients proteins have been recovered from a wide range of archaeological materials, including bones, teeth, eggshells, leathers, parchments, ceramics, painting binders and well-preserved soft tissues like gut intestines. These preserved proteins have provided valuable information about taxonomic identification, evolution history (phylogeny), diet, health, disease, technology and social dynamics in the past.
Bradley Lether Pentelute is currently a professor of chemistry at the Massachusetts Institute of Technology (MIT). His research program lies at the intersection of chemistry and biology and develops bioconjugation strategies, cytosolic delivery platforms, and rapid flow synthesis technologies to optimize the production, achieve site-specific modification, enhance stability, and modulate function of a variety of bioactive agents. His laboratory successfully modified proteins via cysteine-containing “pi-clamps” made up of a short sequence of amino acids, and delivered large biomolecules, such as various proteins and drugs, into cells via the anthrax delivery vehicle. Pentelute has also made several key contributions to automated synthesis technologies in flow. These advances includes the invention of the world's fastest polypeptide synthesizer. This system is able to form amide bonds at a more efficient rate than standard commercial equipment and has helped in the process of understanding protein folding and its mechanisms. This automated flow technology was recently used to achieve total chemical synthesis of protein chains up to 164 amino acids in length that retained the structure and function of native variants obtained by recombinant expression. The primary goal of his endeavor is to use these processes to create designer biologics that can be used to treat diseases and solve the manufacturing problem for on-demand personalized therapies, such as cancer vaccines.
An Artificial Metalloenzyme (ArM) is a designer metalloprotein, not found in nature, which can catalyze desired chemical reactions. Despite fitting into classical enzyme categories, ArMs also have potential in new-to-nature chemical reactivity like catalysing Suzuki coupling, Metathesis etc., which were never reported among natural enzymatic reactions.
Mei Hong is a Chinese-American biophysical chemist and professor of chemistry at the Massachusetts Institute of Technology. She is known for her creative development and application of solid-state nuclear magnetic resonance (ssNMR) spectroscopy to elucidate the structures and mechanisms of membrane proteins, plant cell walls, and amyloid proteins. She has received a number of recognitions for her work, including the American Chemical Society Nakanishi Prize in 2021, Günther Laukien Prize in 2014, the Protein Society Young Investigator award in 2012, and the American Chemical Society’s Pure Chemistry award in 2003.
A collagen hybridizing peptide (CHP) is a synthetic peptide sequence with typically 6 to 10 repeating units of the Gly-Xaa-Yaa amino acid triplet, which mimics the hallmark sequence of natural collagens. A CHP peptide usually possesses a high content of proline and hydroxyproline in the Xaa and Yaa positions, which confers it a strong propensity to form the collagen's unique triple helix conformation. In the single-stranded (monomeric) status, the peptide can recognize denatured collagen strands in tissues by forming a hybridized triple helix with the collagen strands. This occurs via the triple helical chain assembly and inter-chain hydrogen bonding, in a manner similar to primers binding to melted DNA strands during PCR. The binding does not depend on a specific sequence or epitope on collagen, enabling CHPs to target denatured collagen chains of different types.
Hanoch Senderowitz is an Israeli chemist specializing in the fields of Computational Chemistry, Molecular modelling, Computer-Aided Drug Design, and Chemoinformatics.
Jean Baum is an American chemist. She is the distinguished professor of chemistry and chemical biology at Rutgers University, where she is also vice dean for research and graduate education in the school of arts and sciences, and also vice chair of the department of chemistry and chemical biology. Her research investigates protein–protein interaction and protein aggregation using nuclear magnetic resonance spectroscopy (NMR) and other biochemical and biophysical techniques. She serves as treasurer for the Protein Society.
Alexander M. Spokoyny is an American chemist and a professor in chemistry and biochemistry at UCLA and a faculty member of the California NanoSystems Institute (CNSI). He is currently a department chair of Chemistry and Biochemistry at UCLA.
