Chp. 4- The Three Dimensional Structure of Proteins

Conformations

a spatial arrangement of substituent groups that are free to assume different positions in space without breaking any bonds, because of the freedom of bond rotations

How are protein structures stabilized?

By noncovalent interactions and forces

What are the regular secondary structures that protein segments can adopt?

• alpha-helix

• beta-sheet

The tertiary structure describes…

the 3D fold adopted by a protein

How is tertiary structure determined?

by the AA sequence

Native

the biologically active conformation of a macromolecule

Stability

the tendency of a protein to maintain native conformation

There are two rules for structural proteins

1. hydrophobic residues are largely buried in the protein interior

2. the number of hydrogen bonds and ionic interactions within the protein is maximized, thus decreasing the number of unpaired hydrogen bonding and ionic groups

Secondary Structure

the local spatial arrangement of the main-chain atoms in a segment of a polymer (polypeptide or polynucleotide) chain

Alpha-Helix

a helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins

What is the intrinsic property of most amino acid residues?

to form an alpha-helix secondary structure

What are the five types of constraints that affect the stability of the alpha-helix?

1. the intrinsic propensity of an amino acid residue to form an alpha helix

2. the interactions between R-groups

3. the bulkiness of adjacent R-groups

4. the occurrence of Pro and Gly residues

5. interactions between amino acid residues at the ends of the helical segment and the electric dipole inherent to the alpha helix

Beta-Conformation

a spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of rotation

Beta-Sheet

the side-by-side, hydrogen bonded arrangement of polypeptide chains in the extended beta conformation

Beta-turns

a type of secondary structure consisting of four amino acid residues arranged into a tight turn so that the polypeptide turns back on itself

Circular Dichroism (CD) Spectroscopy

a method used to characterize the degree of folding in a protein, based on differences in the absorption of right-handed or left-handed polarized light

Tertiary Structure

the three-dimensional conformation of a polymer in its native, folded structure

Quaternary Structure

the three-dimensional structure of a multisubunit protein, particularly the manner in which the subunits fit together

Fibrous Proteins

insoluble proteins that serve a protective or structural role; contain polypeptide chains that generally share a common secondary structure

Globular Proteins

soluble proteins with a globular shape

Intrinsically Disordered Proteins

proteins or segments that lack a definable three-dimensional structure in a solution. In some cases folding can be dictated by binding partners.

What are the protein structures that provide support, shape and external protection to vertebrates?

Fibrous Proteins

What type of proteins are most enzymes?

Globular Proteins

What is the structure of regulatory proteins?

can be globular, disordered, or contain both

Motif

aka a fold, any distinct folding pattern for elements of secondary structure, observed in one or more proteins. A motif can be simple or complex, and can represent all or just a small part of a polypeptide chain. Also called a fold or supersecondary structure.

Domain

a distinct structural unit of a polypeptide; domains may have separate functions and may fold as independent compact units

The First Rule of Common Protein Folding

the hydrophobic effect makes a large contribution to the stability of protein structures. Burial of hydrophobic amino acid R groups so as to exclude water requires at least two layers of secondary structure.

The Second Rule of Common Protein Folding

Where they occur together in a protein, alpha-helices and beta-sheets generally are found in different structural layers. This is because the backbone of a polypeptide segment in the beta conformation cannot readily hydrogen bond to an alpha helix that is adjacent to it.

The Third Rule of Common Protein Folding

Segments adjacent to each other in the amino acid sequence are usually stacked adjacent to each other in the folded structure. Distant segments of a polypeptide may come together in the tertiary structures but this is not the norm.

The Fourth Rule of Common Protein Folding

The beta-conformation is the most stable when the individual segments are twisted slightly in a right handed sense

Topology Diagram

A structural representation in which the connections between elements of secondary structure are depicted in two dimensions

Oligomer

a short polymer, usually of amino acids, sugars or nucleotides; the definition of “short” is somewhat arbitrary but usually fewer than 50 subunits

Protomer

a general term describing any repeated unit of one or more stably associated subunits in a larger protein structure. In a protomer with multiple subunits, the subunits may be identical or different.

Proteostasis

the maintenance of a cellular-steady state collection of proteins that are required for cell functions under a given set of conditions

Denaturation

Partial or complete unfolding of the specific native conformation of a polypeptide chain, protein or nucleic acid such that the function of the molecule is lost

Renaturation

the refolding of an unfolded (denatured) globular protein so as to restore its native structure and function

Chaperonins

One of two major classes of chaperones in virtually all organisms; a complex of proteins that functions in protein folding: GroES/GroEL in bacteria; Hsp60 in eukaryotes

Chaperones

any of several classes of proteins or protein complexes that catalyze the accurate folding of proteins in all cells

Amyloidoses

a variety of progressive diseases characterized by abnormal deposits of misfolded proteins in one or more tissues

X-Ray Crystallography

the analysis of x-ray diffraction patterns of a crystalline compound used to determine the molecule’s three dimensional structure

Nuclear Magnetic Resonance (NMR)

a technique that utilizes certain quantum mechanical properties of atomic nuclei to study the structure and dynamics of the molecules of which the nuclei are a part

Cryo-electron Microscopy (Cryo-EM)

a technique for determining the structure of proteins or protein complexes; molecules are quick frozen on a grid in random orientations and visualized by EM

In ‘H NMR spectroscopy, which factor determines the shape of the spectra?

the transition between a proton’s alpha and beta spin states

What type of electromagnetic radiation do NMR instruments use to excite atomic nuclei?

radiofrequency radiation

Why are chemical shifts in NMR spectroscopy expressed in units of ppm?

The frequency of a chemical shift depends on the operating frequency of the instrument

What is the physical result of this energy absorption, in NMR spectroscopy?

inversion of nuclear spin states and promotion

Select the number of possible for the magnetic poles of protons in the presence of a magnetic field in ‘H NMR spectroscopy?

2

Select the naturally occurring isotope that does not have a nuclear spin of ± 1/2 .

³²P

Select the naturally occurring isotope that has a nuclear spin of zero, and therefore cannot be monitored via NMR spectroscopy.

¹⁶O

What information can be obtained by integrating the peaks of a ‘H NMR spectrum?

the number of equivalent hydrogen atoms that produce the signal

What unique information can NOESY spectra provide about macromolecules?

the proximity of a proton to other protons in a molecule

Rotation about which bond changes the dihedral angle designated φ?

N-C(alpha)

What are the chromophores detected by circular dichroism (CD) spectroscopy of a protein?

peptide bonds

Which answer choice describes the quaternary structure of hemoglobin?

a pair of alpha-beta protomers; four heme groups

What is proteostasis?

the continuous maintenance of an active set of cellular proteins

What was Eva Nogale’s and Kathleen Collins’s major contribution to structural biology?

the structure of telomerase using cryo-electron microscopy (cryo-EM)

A change in ______ changes the spatial arrangement of atoms in a protein, but does not involve the breaking of covalent bonds.

conformation

Which amino acid has the greatest tendency to form an alpha helix?

alanine

Which vitamin deficiency leads to problems with collagen synthesis?

Vitamin C

Which statement regarding structural biology is FALSE?

It enables protein sequence determinations based on protein function

Which answer choice describes collagen?

left-handed helix; forms triple stranded fibers wrapped in a right handed fashion

Models that assist the folding of proteins are called…

chaperones

What is the electron density map?

a representation of protein structure constructed from the x-ray diffraction pattern

Which bond limits the range of conformation available for a polypeptide chain?

C-N

How many amino acids are in a 6.2 nm long alpha helix?

41

What does it mean for two proteins to be in the same protein family?

the proteins either have similar primary structures and/or similar functions and tertiary structures

What is the function of a chaperone protein?

they interact with partially folded or improperly folded polypeptides to facilitate correct folding pathways

Which statement does NOT describe one of the challenges for analyzing the structure of protein crystals using x-ray crystallography?

Even large proteins are smaller than the wavelength of light, making resolution problematic

What is the effective distance of van der waals forces as atoms approach each other?

0.3 nm to 0.6 nm

The alpha-helix is…

affected by the identities of the residues near each ed

Which answer choice is NOT a characteristics of unstructured proteins?

low charge density

What is the mechanism for protein denaturation by organic solvents and detergents

disrupting nonpolar amino acid side chain interactions

If you wanted to perform structural studies with human telomerase enzyme, one of the largest molecular complexes in the cell, which method would be BEST?

cry-electron microscopy (cryo-EM)

In general, the protein conformation with the lowest free energy has…

the highest number of weak interactions

Estimate the number of amino acids in a typical alpha helix that is 30 A long?

20 AA

Which property is NOT shared by all globular proteins?

proline residues required for peptide chain bending in folds

Which statements regarding the Hsp70 protein family is FALSE?

These proteins are necessary for the growth of some bacterial viruses

How does genetic engineering aid the translation of 2D NMR spectra into a 3D protein structure?

comparing the original spectra to the genetically engineered spectra aids the individual signal assignments

How do “pharmacological chaperones” work?

they correct certain misfolding events in the membrane-bound CFTR protein

How might an ion pair destabilize a protein?

charged amino acids interact with water in the unfolded protein

Which statement is TRUE regarding the oligomeric protein hemoglobin?

The quaternary structure consists of two alpha subunits and two beta subunits

Circular Dichroism (CD) spectroscopy measures the difference between…

absorption of right circular polarized light and absorption of left circular polarized light

How do aromatic residues affect the formation of amylase fibrils?

they stabilize the protein structure such that fibrils form more slowly and disease onset occurs later in life

All of these diseases are examples of amyloid diseases except…

cystic fibrosis

Circular dichroism (CD) spectroscopy can do all of the following except…

determine the primary structure of proteins

If a disulfide bond connects two polypeptide chains in a protein, the highest level of protein organization this protein has…

quaternary structure

Denaturing followed by renaturing of a protein..

demonstrates that primary structure dictates tertiary structure

Which statement is true concerning disulfide bonds?

Disulfide bond formation is more likely outside of the cell