Introduction To Protein Structure (2nd Edition Pdf Free Download) [EXCLUSIVE]

Introduction to Protein Structure provides an account of the principles of protein structure, with examples of key proteins in their biological context generously illustrated in full-color to illuminate the structural principles described in the text. The first few chapters introduce the general principles of protein structure both for novices and for non-specialists needing a primer. Subsequent chapters use specific examples of proteins to show how they fulfill a wide variety of biological functions. The book ends with chapters on the experimental approach to determining and predicting protein structure, as well as engineering new proteins to modify their functions.

Carl Branden was educated at Uppsala University (PhD) and the MRC Laboratory for Molecular Biology, Cambridge, where he was a postdoctoral fellow in the laboratory of J.C. Kendrew. He has pursued a career in basic research, science administration (as science advisor to the Swedish Government), and biotechnology. Formerly Research Director of the European Synchrotron Radiation Facility in Grenoble, France, he is now at the Microbiology and Tumor Biology Center at the Karolinska Institute in Stockholm. A protein crystallographer with a distinguished academic career in research and teaching, he has made major contributions to the understanding of many biological structures, and is an editor of Structure.

Introduction To Protein Structure (2nd Edition Pdf Free Download)

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"As an introduction to what proteins look like, how they fold up and how they interact with other molecules, large and small this book has no peer. It will be invaluable to students and research workers." Trends in Biotechnical Sciences

The VitalBook e-book of Introduction to Protein Structure, Second Edition is inly available in the US and Canada at the present time. To purchase or rent please visit to Protein Structure provides an account of the principles of protein structure, with examples of key proteins in their bio

In this course, an introduction to protein and nucleic acid structures is delivered through various lectures, as well as exploring the relationship between protein structures and common human pathologies.

Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated with student learning, it is quite challenging to develop visualizations that allow students to interactively observe the effects of altered amino acid sequence on protein structure. A software simulation, the protein investigator (PI), has been developed to specifically facilitate this type of exploration. When using the PI, students enter or edit an amino acid sequence; the software then simulates its folding in two dimensions using the major forces involved in protein structure. This study explores freshman undergraduate students' use of visualization and simulation when learning about protein structure. It also evaluates some of the learning outcomes from these two approaches. Our results show that simulation leads to similar learning outcomes as visualization. Because simulation allows a more interactive exploration, a combination of the two approaches may be an effective approach to introducing the basic principles of protein structure.

Proteins are polypeptide structures consisting of one or more long chains of amino acid residues. They carry out a wide variety of organism functions, including DNA replication, transporting molecules, catalyzing metabolic reactions, and providing structural support to cells. A protein can be identified based on each level of its structure. Every protein at least contains a primary, secondary, and tertiary structure. Only some proteins have a quaternary structure as well. The primary structure is comprised of a linear chain of amino acids.

The secondary structure contains regions of amino acid chains that are stabilized by hydrogen bonds from the polypeptide backbone. These hydrogen bonds create alpha-helix and beta-pleated sheets of the secondary structure. The three-dimensional shape of a protein, its tertiary structure, is determined by the interactions of side chains from the polypeptide backbone. The quaternary structure also influences the three-dimensional shape of the protein and is formed through the side-chain interactions between two or more polypeptides. Each protein at least contains a primary, secondary, and tertiary structure. Only some proteins have a quaternary structure as well.

To reiterate, the primary structure of a protein is defined as the sequence of amino acids linked together to form a polypeptide chain. Each amino acid is linked to the next amino acid through peptide bonds created during the protein biosynthesis process. The two ends of each polypeptide chain are known as the amino terminus (N-terminus) and the carboxyl terminus (C-terminus). Twenty different amino acids can be used multiple times in the same polypeptide to create a specific primary protein structure sequence.

In any cell, the DNA preserves the code used to synthesize proteins. The nucleotide sequence of a protein-encoding gene is transcribed into another nucleotide sequence (RNA transcript or mRNA), which is then used to synthesize a sequence of amino acids to form a protein. This is historically known as the Central Dogma. RNA polymerases transcribe genes.

The A site is the first binding site where the initial incoming aminoacyl tRNA pairs with its codon. As the second aminoacyl tRNA binds to the A site, the initial tRNA molecule shifts to the adjacent P site. As the shift happens, the amino acid attached to the tRNA molecule in the P site forms a peptide bond to the amino acid in the A site. This leaves the tRNA at the P site deacylated while tRNA at the A site carries the peptide chain. The deacylated tRNA moves into the E site and gets released as the tRNA in the A site moves over to the P site. The P site holds the tRNAs linked to the growing polypeptide chain. Then a new tRNA molecule attaches to the codon in the unoccupied A site. The codons UAG, UGA, and UAA are used to end the protein translation (termination codons). The process of adding amino acids to the chain is repeated until a stop codon is reached.

Each amino acid consists of a carboxyl group, an amino group, and a side chain. Amino acids are linked together by joining the amino group of one amino acid with the carboxyl group of the adjacent amino acid. Each amino acid side chain has differing properties. Some side chains can be either acidic or basic, while others can be polar uncharged or just non-polar. These characteristics provide insight into whether the protein generally functions better in acidic or basic environments, solubility in water or lipids, the temperature range for optimal protein function, and which parts of the protein are found on the protein interior being in contact with the external aqueous environment. Some amino acids contained within the polypeptide chain can even create ionic bonds and disulfide bridges. The location of certain amino acids in the primary structure dictates how the secondary, tertiary, and quaternary structure will look.

Splicing occurs within the nucleus. Several steps are catalyzed by large (60S) molecules called spliceosomes composed of small ribonucleoproteins (snRNPs) and splicing factors. These enzymes excise the introns out of the mRNA transcript while leaving exons in the transcript alone. Spliceosomes shuffle around these exons, depending on the type of protein that needs to be synthesized.

This method is used to find the sequence of amino acids of a protein.[18] Essentially, the amino-terminal residue is labeled and cleaved from the polypeptide chain without disturbing the peptide bonds that hold together other amino acid residues. This process repeats by cleaving off one amino acid at a time until the entire chain is sequenced. Due to this method's tedious nature, a protein sequenator can be used to perform the Edman degradation in an automated way.

Amino acid sequencing of peptides can be performed through mass spectrometry.[19] Although this technique gains limited data from analyzing entire proteins at a time, it can effectively analyze peptides. One method of using mass spectrometry is called peptide mass fingerprinting (PMF). PMF is widely used to identify single purified proteins but is not feasible for heterogeneous protein mixtures.[20] A generalized procedure of this method is as follows:

The genetic defect of SCA is found within the beta globulin gene. Both the normal and mutated protein products consist of 147 amino acids. However, the mutated beta globulin protein has a single-base substitution (point mutation) at the sixth amino acid in the chain. In the sickle cell gene, GTG (the codon for valine) replaces the normal GAG codon (for glutamic acid).[23] This defect deforms the normal biconcave disc shape of red blood cells into a crescent or sickle shape instead. Symptoms include anemia, episodes of pain, organ damage, delayed growth, and swelling of the hands and feet.[24][25]

Disease-causing mutations within the CFTR gene alter the protein structure, thus impairing chloride ion transport. Normally, this protein transports chloride ions in and out of cells that produce saliva, sweat, tears, mucus, and digestive enzymes. Due to the impaired chloride ion transport, cells that line the passageways of the pancreas, lungs, and other organs start producing abnormally thick and sticky mucus. In turn, the abnormal mucus production obstructs the airways and glands. CF symptoms include salty sweat/salty-tasting skin, exocrine pancreatic insufficiency, chronic pneumonia, lung fibrosis, obstructive azoospermia, and accumulation of thick, sticky mucus.[27][28]

Identification of the specific base-pair mutations within the gene can help healthcare professionals further understand the disease phenotype of the patient. The severity of each disease is dependent on a few factors, such as the function of the protein, how many amino acids are involved with the base-pair mutation, and the type of mutation. For example, a base pair substitution that leads to a silent mutation will not change any part of the amino acid sequence. On the other hand, an insertion or deletion of 1 or 2 base pairs leads to a frameshift mutation. After the frameshift mutation translates, all codons lead to a different amino acid composition of the polypeptide chain, which normally leads to a nonfunctional protein. A mutated protein with an insertion or deletion of exactly 3 base pairs (or multiples of 3 base pairs) can have varied functionality. e24fc04721