protection factors provide information on the stability of individual amino acids in proteins. why is the...

protection factors provide information on the stability of individual amino acids in proteins. why is the determination of protection factors not possible using HDX-MS?

Solutions

Expert Solution

Ans . HDX (Hydrogen / deuterium exchange ) monitered by MS (mass spectrometry) is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time-dependent change in the mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens, but determining the latter from the former is generally not possible.

The key to interpreting HDX kinetics is the fact that exchange occurs faster for amides that are solvent exposed and / or not involved in hydrogen bonds.

HDX-MS relies on the measurable difference of mass between the deuterated and nondeuterated polypeptide chains. To obtain more specific information, the polypeptide is further fragmented by proteolysis at a low pH and a low temperature. Under MS analysis conditions, deuterium incorporated into exchangeable side chain groups and N - terminal amines is rapidly back exchanged , and as a consequence , HDX- MS is only sensitive to the backbone amide exchange.

HDX-MS yields the overall mass change over time for a whole peptide fragment ( usually presented as a centroid of the isotopic envelope ) but does not provide direct information on the exchange rate of individual residues.

The ratio of observed exchange rate to the maximal one ( i.e., that measured for a completely unstructured peptide ) is the so called protection factor. Protection factors contain both structural and dynamic information ; the degree of protection of amide hydrogen from solvent deuterium correlates to the degree of involvement in secondary and tertiary structure.

gladiator answered 1 year ago

Next > < Previous

Related Solutions

The 21st and 22nd amino acids found in proteins are the rare amino acids ______________ and...

The 21st and 22nd amino acids found in proteins are the rare amino acids ______________ and ______________. ________________ are nonviral genetic elements that have reverse transcriptase activity. An example of retrotransposons in the human genome is the ____ family of sequences.

Proteins are chains of amino acids. There are twenty different types of naturally occurring amino acids,...

Proteins are chains of amino acids. There are twenty different types of naturally occurring amino acids, and all organisms must have all twenty of them in order to survive. In this project we will be discussing the amino acid leucine. What are the two possible methods that a cell may employ to be certain that it has each of the 20 amino acids? RNA is partly made of the base uracil. What are the two possible methods that a cell...

Common proteins are polymers of 20 different amino acids. How many amino acids are necessary for...

Common proteins are polymers of 20 different amino acids. How many amino acids are necessary for a protein polymer to have at least as many possible different sequences as there are atoms in the Universe? (There are about 2 × 1056 moles of atoms in the Universe.) *Note - The answer is a mathmatical answer. I need an explanation of the math behind this problem.

Proteins are ______________ built from amino acids, which each have an amino group

Proteins are ______________ built from amino acids, which each have an amino group and a _____________ group attached to the central _______________. There are twenty possible _______________ that differ in structure and are generally referred to as “R.” In solutions of neutral pH, amino acids are _______________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together through _______________, which are formed by condensation reactions between the carboxyl end of the last amino...

If peptidases digest proteins into amino acids, why don’t they auto-digest the cells where they are...

If peptidases digest proteins into amino acids, why don’t they auto-digest the cells where they are synthesized?

The structure and properties of amino acids determine the structure and properties of proteins and, therefore,...

The structure and properties of amino acids determine the structure and properties of proteins and, therefore, their function. How do amino acids and peptide properties dictate protein structure and function? In your explanation, please include the key terms hydrophobicity, hydrogen bonding, electrostatic interactions, acid-base property.

The structure and properties of amino acids determine the structure and properties of proteins and, therefore,...

The structure and properties of amino acids determine the structure and properties of proteins and, therefore, their function. How do amino acids and peptide properties dictate protein structure and function? In your explanation, please include at least one representation and the key terms hydrophobicity, hydrogen bonding, electrostatic interactions, acid-base property

Amino acids are the building blocks of proteins, and can act as both a Brønsted acid...

Amino acids are the building blocks of proteins, and can act as both a Brønsted acid and a Brønsted base through intramolecular proton transfer (see Chapter 16, pg. 709 of the textbook). The simplest amino acid known is glycine, NH2CH2CO2H (Ka = 4.5 ×10–3 and Kb = 6.0 ×10–5 ), and it can exist in three forms in equilibrium with one another: H2N––CH2––COOH +H3N––CH2––COOH +H3N––CH2––COO– H2N––CH2––COO– Glycine cation zwitterion anion (a) Write the equilibria corresponding to Ka and Kb of...

3) Proteins are made up of amino acids as the building blocks. a) The structural integrity...

3) Proteins are made up of amino acids as the building blocks. a) The structural integrity of a protein is critical for its functions. Using no more than 300 words, describe TWO (2) examples of mutations or alterations to the native protein sequence which have led to an enhancement or reduction in the biological activity of the mutant proteins. For example, enzyme kinetics, antimicrobial activity, anticancer, drug interaction, and others. (Note: Must only be based on recent (<5 years) research...

What is false? Proteins are made of long strings of 20 different common amino acids in...

What is false? Proteins are made of long strings of 20 different common amino acids in different orders. The chemical properties of each amino acid are determined by the amino acid's side chain. The order of amino acids in a polypeptide determines the three-dimensional shape of the folded molecule. Most proteins consist of two amino acid polymers attached together by hydrogen bonding.

Subjects