File Name: introduction to proteins structure function and motion .zip
Proteins are crucial to the functioning of all lifeforms. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination.
This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. He received his Ph. He has authored many research and review articles and book chapters in the fields of medicinal research, molecular modeling, drug design, and systems biology.
Proteins are large biomolecules or macromolecules that are comprised of 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. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20—30 residues, are rarely considered to be proteins and are commonly called peptides , or sometimes oligopeptides.
The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene , which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea — pyrrolysine.
Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins.
Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover.
A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1—2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells.
Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling , immune responses , cell adhesion , and the cell cycle.
In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation , precipitation , electrophoresis , and chromatography ; the advent of genetic engineering has made possible a number of methods to facilitate purification.
Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry. Proteins were recognized as a distinct class of biological molecules in the eighteenth century by Antoine Fourcroy and others, distinguished by the molecules' ability to coagulate or flocculate under treatments with heat or acid.
Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a nearly correct molecular weight of Da. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh.
Working with Lafayette Mendel and applying Liebig's law of the minimum in feeding laboratory rats , the nutritionally essential amino acids were established. The work was continued and communicated by William Cumming Rose. The understanding of proteins as polypeptides came through the work of Franz Hofmeister and Hermann Emil Fischer in Sumner showed that the enzyme urease was in fact a protein.
The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, e.
In the s, the Armour Hot Dog Co. Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding , an idea first put forth by William Astbury in The first protein to be sequenced was insulin , by Frederick Sanger , in Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids , or cyclols.
The first protein structures to be solved were hemoglobin and myoglobin , by Max Perutz and Sir John Cowdery Kendrew , respectively, in The number of proteins encoded in a genome roughly corresponds to the number of genes although there may be a significant number of genes that encode RNA of protein, e. Viruses typically encode a few to a few hundred proteins, archaea and bacteria a few hundred to a few thousand, while eukaryotes typically encode a few thousand up to tens of thousands of proteins see genome size for a list of examples.
Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO—NH amide moiety into a fixed conformation. Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.
The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar.
The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. The words protein , polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation , whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20—30 residues.
Proteins can interact with many types of molecules, including with other proteins , with lipids , with carboyhydrates , and with DNA.
It has been estimated that average-sized bacteria contain about 2 million proteins per cell e. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50, to 1 million.
By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion.
For instance, of the 20, or so proteins encoded by the human genome, only 6, are detected in lymphoblastoid cells. Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein.
The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG adenine — uracil — guanine is the code for methionine.
Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. Most organisms then process the pre-mRNA also known as a primary transcript using various forms of Post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid.
In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm , where protein synthesis then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.
The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes.
The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus. The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass , which is normally reported in units of daltons synonymous with atomic mass units , or the derivative unit kilodalton kDa. The average size of a protein increases from Archaea to Bacteria to Eukaryote , , residues and 31, 34, 49 kDa respectively due to a bigger number of protein domains constituting proteins in higher organisms.
Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis , which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. Chemical synthesis is inefficient for polypeptides longer than about amino acids, and the synthesized proteins may not readily assume their native tertiary structure. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. The shape into which a protein naturally folds is known as its native conformation.
Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions.
In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as " conformations ", and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site , or the physical region of the protein that participates in chemical catalysis.
In solution proteins also undergo variation in structure through thermal vibration and the collision with other molecules. Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins , fibrous proteins , and membrane proteins.
Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, such as collagen , the major component of connective tissue, or keratin , the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane.
A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration , are called dehydrons. Many proteins are composed of several protein domains , i. Domains usually also have specific functions, such as enzymatic activities e. Short amino acid sequences within proteins often act as recognition sites for other proteins. Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.
The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly.
The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine.
Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of the same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein—protein interactions also regulate enzymatic activity, control progression through the cell cycle , and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function.
Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks. The best-known role of proteins in the cell is as enzymes , which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification.
About 4, reactions are known to be catalysed by enzymes. The molecules bound and acted upon by enzymes are called substrates.
Ewalt, Karla L. Manning, James M. Last reviewed: March A polymeric compound made up of various monomeric units called amino acids joined by peptide linkages. Proteins are central to the processes of life. They are fundamental components of all biological systems, performing a wide variety of structural and functional roles.
Proteins are large biomolecules or macromolecules that are comprised of 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. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide.
Protein structural comparison is an important operation in molecular biology and bionformatics. It plays a central role in protein analysis and design. As proteins fold in three dimensional space, assuming a variety of shapes, a careful characterization of their geometry is needed to study their function which is known to be related to the shape. Moreover, the comparison of protein structures is essential to infer evolutionary information. Unable to display preview. Download preview PDF. Skip to main content.
Jetzt bewerten Jetzt bewerten. Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, …mehr.
It seems that you're in Germany. We have a dedicated site for Germany. This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. He received his Ph. He has authored many research and review articles and book chapters in the fields of medicinal research, molecular modeling, drug design, and systems biology.
Тонкие губы Клушара изогнулись в понимающей улыбке. - Да, да, конечно… очень приятно. - Так вы гражданин Канады.
Быть может, смерть Танкадо в публичном месте была необходимостью, однако публика возникла чересчур. Халохот был вынужден скрыться, не успев обыскать убитого, найти ключ. А когда пыль осела, тело Танкадо попало в руки местной полиции.
Халохот сразу же увидел Беккера: нельзя было не заметить пиджак защитного цвета да еще с кровавым пятном на боку. Светлый силуэт двигался по центральному проходу среди моря черных одежд. Он не должен знать, что я. - Халохот улыбнулся. - Может считать себя покойником.
Сьюзан заставила себя промолчать. Хейл хмыкнул себе под нос и убрал упаковку тофу. Затем взял бутылку оливкового масла и прямо из горлышка отпил несколько глотков.
Как скажете. - Лейтенант направился к двери. - Я должен выключить свет. Беккер держал коробку под мышкой. Я ничего не упустил.
А метод грубой силы? - предложил Бринкерхофф. - Можно ли с его помощью найти ключ.
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Introduction to Proteins: Structure, Function, and Motion (Chapman & Hall/CRC Mathematical and Computational Biology). December DOI.