Protein Chemistry. Structure, Properties, and Research Methods - Shendryk A.N. 2022

Protein Structure
Spatial Structure of Proteins
Secondary Protein Structure - Helical Structures

A specific type of spatial orientation of the peptide chain results from various modes of free rotation around the bonds connecting a-carbon atoms. Natural Peptides and Proteins feature three MAIN TYPES OF Secondary Structure:

> helix;

> pleated sheet;

> random coil.

The helical and planar forms represent ordered structures, whereas the random coil is disordered.

The ordered arrangement of a protein chain exhibits a clearly distinct orientation characterized by uniform rotation angles φ and ψ. Peptide chains can form both left- and right-handed helices (left- and right-handed spirals), see Fig. 2.1.

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Fig. 2.1 Fragments of peptide chains with left- and right-handed helices. R-residues are positioned perpendicular to the plane of the drawing.

For peptide chains composed of L-Amino Acids, the right-handed helix is energetically more favorable, whereas D-amino acid residues preferentially form the left-handed helix. The existence of Helical structures in protein chains was first proven by Pauling and Corey in 1951 (see Fig. 2.2).

Fig. 2.2 The Pauling-Corey model of the a-helix

In 1954, Pauling was awarded the Nobel Prize in Chemistry for his research into The Nature of the chemical bond and its application to The structure of proteins. In 1962, he was awarded the Nobel Peace Prize.

PAULING, Linus C.

February 28, 1901 – August 19, 1994

Nobel Prize in Chemistry, 1954

Nobel Peace Prize, 1962

The American chemist Linus Carl Pauling was born in Portland, Oregon, into the family of a pharmacist. Pauling Sr. died when his son was nine years old. From early childhood, P. was fascinated by science. He initially collected insects and minerals. At the age of 13, one of P.'s friends introduced him to chemistry, and the future scientist began conducting experiments. He did this at home, using glassware borrowed from his mother's kitchen. P. attended Washington High School in Portland but did not graduate with a diploma. Nevertheless, he enrolled at Oregon Agricultural College (later Oregon State University) in Corvallis, where he majored in chemical engineering, chemistry, and physics. To support himself and his mother financially, he worked odd jobs washing dishes and sorting paper. During his junior year, recognized as an exceptionally gifted student, P. was appointed an assistant in the Department of Analytical Chemistry. In his senior year, he served as a teaching assistant in chemistry, mechanics, and Materials. After receiving a Bachelor of Science degree in chemical engineering in 1922, P. began working toward his doctorate in chemistry at the California Institute of Technology in Pasadena.

P. was the first student at the California Institute of Technology to transition immediately from graduation to a position as an assistant and then an instructor in the chemistry department. In 1925, he earned his doctorate in chemistry summa cum laude. Over the next two years, he worked as a research fellow and member of the National Research Council at Caltech. In 1927, P. was appointed assistant professor, in 1929 associate professor, and in 1931 professor of chemistry.

Continuing his research throughout these years, P. became an expert in X-ray crystallography. Using this technique, he investigated the nature of chemical bonding in benzene and other Aromatic Compounds. A Guggenheim Fellowship enabled him to spend the 1926/1927 academic year studying quantum mechanics with Arnold Sommerfeld in Munich, Erwin Schrödinger in Zurich, and Niels Bohr in Copenhagen.

In 1928 (at the age of 27), P. put forward his theory of Resonance, or Hybridization, of chemical bonds in aromatic compounds, which was based on the quantum-mechanical concept of electron orbitals. In the older model of benzene, which was still occasionally used for convenience, three of the six chemical bonds (representing electron pairs) between adjacent carbon atoms were single bonds, while the remaining three were double bonds. Single and double bonds alternated within the benzene ring. Consequently, benzene could theoretically possess two possible structures depending on the placement of single and double bonds. However, it was known that double bonds are shorter than single bonds, whereas X-Ray Diffraction demonstrated that all bonds within the molecule are of equal length. The resonance theory postulated that all carbon-carbon bonds in the benzene ring are intermediate in character between single and double bonds. According to P.'s model, benzene rings can be regarded as hybrids of their contributing structures. This concept proved extremely valuable for predicting The properties of aromatic compounds.

Over the next several years, P. continued to study the PHYSICOCHEMICAL PROPERTIES OF molecules, particularly those related to resonance. In 1934, he turned his attention to biochemistry, specifically Protein Biochemistry. In collaboration with A.E. Mirsky, he formulated a theory of protein Structure and function, and together with C.D. Coryell, he investigated The Effect of oxygenation on the magnetic properties of Hemoglobin.

When Arthur Noyes died in 1936, P. was appointed chairman of the Division of Chemistry and Chemical Engineering and director of the Gates and Crellin Chemical Laboratories at Caltech. In these administrative roles, he initiated the investigation of the atomic and molecular structure of PROTEINS AND AMINO acids using X-ray crystallography.

In 1942, P. and his colleagues produced the first artificial Antibodies, successfully altering the Chemical Structure of certain Blood proteins known as globulins. P. correctly postulated that the three-dimensional structures of an antigen and its antibody are complementary and thus "responsible" for The formation of the antigen-antibody complex. In 1947, he and George W. Beadle received a grant to conduct a five-year study on the mechanism by which the poliovirus destroys Nerve Cells.

P.'s research on Sickle-Cell Anemia began in 1949 when he learned that THE RED BLOOD cells of patients with this hereditary disease assume a sickle shape only in venous blood, where oxygen levels are low. Drawing on his knowledge of hemoglobin chemistry, P. immediately hypothesized that the sickling of red cells is caused by a genetic defect deep within the cellular hemoglobin. This hypothesis stands as a striking testament to the remarkable scientific intuition so characteristic of P. Three years later, the scientist successfully demonstrated that normal hemoglobin and hemoglobin from sickle-cell anemia patients can be distinguished by Electrophoresis. This discovery confirmed P.'s conviction that the underlying anomaly resides in the protein portion of the molecule.

In 1951, L. Pauling and R.B. Corey published the first complete Description of the molecular structure of proteins, culminating 14 years of rigorous research. Utilizing X-ray crystallography to analyze proteins found in Hair, wool, Muscle, Nails, and other biological Tissues, they discovered that amino acid chains are intertwined to form a helical structure. This breakthrough in elucidating the three-dimensional architecture of proteins marked a major milestone in biochemistry.

However, not all of Pauling's scientific endeavors were met with success. In the early 1950s, he shifted his focus to deoxyribonucleic acid (DNA), the biological molecule that carries METABOLISM/28.html">The Genetic Code. In 1953, as scientists worldwide raced to decipher the structure of DNA, Pauling published a paper proposing an erroneous triple-helix model. Just a few months later, Francis Crick and James D. Watson published their seminal paper revealing the iconic double-helix STRUCTURE OF THE DNA molecule.

In 1954, Pauling was awarded the Nobel Prize in Chemistry “for his research into the Nature of the chemical bond and its application to the elucidation of the structure of complex substances.” In his Nobel lecture, he predicted that future chemists would “rely upon a new structural chemistry, including the precisely determined geometric relationships between atoms in molecules and the rigorous application of new structural principles, and that through this technology, significant progress would be achieved in solving problems in biology and medicine by chemical Methods.”

Despite being a pacifist during his youth amidst the First World War, Pauling served during the Second World War as an official member of the National Defense Research Committee, working on The Development of new rocket propellants and seeking alternative oxygen sources for submarines and aircraft. As a researcher for the Office of Scientific Research and Development, he made significant contributions to the development of plasma expanders for blood transfusion for military needs. However, shortly after the United States dropped atomic bombs on the Japanese cities of Hiroshima and Nagasaki, Pauling launched a campaign against this new class of weapon. In 1945–1946, serving as a member of the National Security Commission, he lectured widely on the hazards of nuclear warfare.

In 1946, Pauling became a co-founder of the Emergency Committee of Atomic Scientists, established by Albert Einstein and seven other renowned scientists to advocate for a ban on atmospheric nuclear weapons testing. Four years later, as the nuclear arms race accelerated, Pauling opposed his government's decision to develop the hydrogen bomb, calling for an absolute halt to all atmospheric nuclear tests. In the early 1950s, following atmospheric hydrogen bomb tests conducted by both the US and the USSR that elevated global Background radiation, Pauling leveraged his formidable oratorical skills to publicize the potential biological and Genetic consequences of radioactive fallout. His concern over these genetic hazards was partly fueled by his ongoing research into the Molecular Basis of Hereditary diseases. In 1955, Pauling and 52 other Nobel laureates signed the Mainau Declaration, urging an end to the arms race.

When Pauling drafted a petition demanding an end to nuclear testing in 1957, it was signed by over 11,000 scientists from 49 countries, including more than 2,000 Americans. In January 1958, Pauling presented this document to Dag Hammarskjöld, then Secretary-General of the United Nations. Pauling's efforts contributed significantly to the ESTABLISHMENT OF THE Pugwash Conferences on Science and World Affairs—whose inaugural meeting took place in 1957 in Pugwash, Nova Scotia, Canada—which ultimately helped pave the way for the Nuclear Test Ban Treaty. This profound public and personal concern over radioactive atmospheric contamination led the US, USSR, and Great Britain to voluntarily suspend atmospheric nuclear testing in 1958, even in the absence of a formal treaty.

However, Pauling's tireless efforts to secure a ban on atmospheric nuclear testing met not only with support but also with fierce opposition. Prominent American scientists such as Edward Teller and Willard F. Libby, both members of the US Atomic Energy Commission, argued that Pauling was exaggerating the biological impact of radioactive fallout. Pauling also encountered political obstacles due to persistent allegations of pro-Soviet sympathies.

Ironically, during the same period, Pauling came under attack in the Soviet Union as well, where his groundbreaking resonance theory of chemical bonding was denounced as contrary to Marxist doctrine. (Following the death of Joseph Stalin in 1953, the theory was officially rehabilitated in Soviet science.) Pauling was summoned twice (in 1955 and 1960) before the U.S. Senate Internal Security Subcommittee to answer questions regarding his political views and activities. On both occasions, he denied ever being a Communist or harboring Marxist sympathies. During the second Hearing in 1960, risking a citation for contempt of Congress, he refused to disclose the names of those who had assisted him in gathering signatures for the 1957 petition. The case was ultimately dropped.

In June 1961, Pauling and his wife organized a conference in Oslo, Norway, against the spread of nuclear weapons. In September of that year, despite appeals from Pauling to Nikita Khrushchev, the USSR resumed atmospheric nuclear testing, followed by the United States in March of the following year. Pauling began monitoring radiation levels and, in October 1962, publicized data showing that testing over the previous year had doubled atmospheric radioactivity compared to the preceding 16 years. Pauling also drafted a proposed test-ban treaty. In July 1963, the US, USSR, and Great Britain signed the Nuclear Test Ban Treaty, which was largely based on Pauling's draft.

In 1963, Pauling was awarded the 1962 Nobel Peace Prize. In his presentation speech on behalf of the Norwegian Nobel Committee, Gunnar Jahn stated that Pauling had “campaigned unceasingly, not only against nuclear weapons tests, not only against the spread of these armaments, not only against their very use, but against all warfare as a means of solving international conflicts.” In his Nobel lecture, entitled “Science and Peace,” Pauling expressed hope that the nuclear test ban treaty would mark “the beginning of a series of treaties that will bring about a new world where the possibility of war is forever eliminated.”

The same year he received his second Nobel Prize, Pauling retired from the California Institute of Technology and became a research professor at the Center for The Study of Democratic Institutions in Santa Barbara, California. There, he was able to devote more time to issues of international disarmament. In 1967, Pauling also accepted a position as professor of chemistry at the University of California, San Diego, hoping to focus more of his time on molecular medicine research. Two years later, he moved to Stanford University in Palo Alto, California, as professor of chemistry. By this time, Pauling had already stepped down from his position at the Center for the Study of Democratic Institutions.

In the late 1960s, Pauling developed a keen interest in the BIOLOGICAL EFFECTS OF Vitamin C. He and his wife began taking the vitamin regularly, and Pauling started publicly advocating its use to prevent the common cold. In his monograph Vitamin C and the Common Cold, published in 1971, he synthesized practical evidence and theoretical arguments from current literature supporting the therapeutic properties of vitamin C. In the early 1970s, Pauling also formulated The Theory of orthomolecular medicine, which emphasized The Importance of Vitamins and amino acids in maintaining an optimal molecular environment for the Brain. Although widely publicized at the time, these theories were not substantiated by subsequent research and were largely dismissed by medical and psychiatric professionals. Nevertheless, Pauling maintained that the grounds for their counterarguments were far from flawless.

In 1973, Pauling founded the Linus Pauling Institute of Science and Medicine in Palo Alto. He served as its president for the first two years and subsequently became a professor there. He and his colleagues at the institute continued to research the therapeutic properties of vitamins, particularly the potential application of vitamin C in Cancer Treatment. In 1979, Pauling published Cancer and Vitamin C, in which he argued that high doses of vitamin C help prolong life and improve the condition of patients with certain types of cancer. However, authoritative cancer researchers have not found his arguments convincing.

In 1922, Pauling married Ava Helen Miller, one of his students at Oregon Agricultural College. They had three sons and a daughter. Following his wife's death in 1981, Pauling resided at their country home in Big Sur, California.

In addition to his two Nobel Prizes, Pauling received numerous awards and honors. These include the American Chemical Society's Award in Pure Chemistry (1931), the Davy Medal of the Royal Society of London (1947), the Soviet government's International Lenin Peace Prize (1971), the National Medal of Science from the National Science Foundation (1975), the Lomonosov Gold Medal of the USSR Academy of Sciences (1978), the US National Academy of Sciences Award in Chemical Sciences (1979), and the American Chemical Society's Priestley Medal (1984). He was awarded honorary degrees from the University of Chicago, Princeton University, Yale University, Oxford University, and the University of Cambridge. Pauling was a member of numerous professional organizations, including the US National Academy of Sciences and the American Academy of Arts and Sciences, as well as scientific societies and academies in Germany, Great Britain, Belgium, Switzerland, Japan, India, Norway, Portugal, France, Austria, and the USSR. He served as president of the American Chemical Society (1948) and the Pacific Division of the American Association for the Advancement of Science (1942–1945), and as vice-president of the American Philosophical Society (1951–1954).

Source of information:

Nobel Laureates: Encyclopedia: Translated from English. - M.: Progress, 1992.

The theoretically predicted values of the dihedral angles in the most extensively studied right-handed a-helix should be: φ = -58∘, and ψ = -41∘. According to X-ray crystallographic data for A number of proteins, their averaged values are: φ = -62∘, and ψ = -41∘. Such angle values ensure maximum structural stability. This stability is achieved because the structure is virtually free of steric hindrance, particularly for R-side chains (firstly). Secondly, the C=O and N-H dipoles of the peptide bonds are oriented almost coaxially, which is optimal for dipole-dipole interactions and ensures the formation of an extensive system of intramolecular cooperative Hydrogen Bonds. These reliably stabilize the a-helix.

The formation of intramolecular hydrogen bonds is a direct consequence of the planar peptide group being in the trans-form. In the a-helix, each NH group of the peptide chain is hydrogen-bonded to the C=O group of the fourth amino acid, thereby forming a 13-membered ring. Therefore, the a-helix is sometimes designated as a 3.6₁₃-helix (3.6 amino acid residues in a 13-membered ring). If the a-helix is oriented with the N-terminus pointing upward, all C=O groups will point downward, and the NH groups will point upward.

Another characteristic feature of the a-helix follows directly from the combination of the φ and ψ angle values: the pitch of the helix (one complete turn) is 5.4Å, comprising 3.6 amino acid residues per turn. The angle of Rotation of the chain per amino acid residue is: 360∘/3.6 = 100∘. The diameter of the helix (excluding side groups) is 6Å. For L-amino acids, the right-handed helix has the distinct advantage over the left-handed one in that The amino acid R-groups are directed outward from the central axis, which dramatically reduces steric strain. Furthermore, the outwardly oriented R-residues impart hydrophilicity or Hydrophobicity to the peptide chain.

The content of a-helices in Globular proteins varies widely: from a complete absence (such as in snake neurotoxins) to 80–90%. Myoglobin and hemoglobin contain 75% helical regions, serum albumin contains 50%, Ribonuclease 17%, and Chymotrypsin 8%.

A protein cannot have 100% a-helices in its chain and still retain its globular structure; in that case, it would be fibrous. Moreover, when an a-helix is present, it is typically restricted to one, two, or several discrete segments of the chain. The helical structure is disrupted by numerous factors. Examples include the presence of a Proline residue, whose cyclic structure introduces a kink into the peptide chain; local electrostatic repulsion caused by a cluster of positively charged Lysine and Arginine R-groups, or a cluster of negatively charged glutamic and aspartic acid R-groups; and other causes. The non-helical portion of the peptide chain may adopt a pleated sheet structure or a random coil.

In addition to the a-helix, Other types of helices are known. They differ from one another in the number of amino acid residues per turn. For example, the 3₁₀-helix contains three residues in a 10-membered ring, and the 4.3₁₆- or π-helix contains 4.3 amino acid residues in a 16-membered ring. The 3₁₀-helix and π-helix are extremely rare in real proteins and occur only in very short segments of the peptide chain (for instance, in myoglobin and Lysozyme). Left-handed 3₁₀- and π-helices have not yet been discovered in natural proteins.