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PDB-101: Video Challenge 2020

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Molecular explorations
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Mechanisms of
Bacterial Resistance
to Aminoglycoside Antibiotics

2019 RCSB PDB Video Challenge for High School Students

2019 Video Challenge Awards

For the sixth year, RCSB PDB invited high school students to tell molecular stories in video. The 2019 challenge focused on the molecular mechanisms behind bacterial resistance to aminoglycoside antibiotics. See Challenge Details.

The video submission opened on January 15, 2019 and concluded on April 23, 2019. Award winners were announced at rcsb.org on May 14, 2019.

The challenge entries (available online) demonstrate many creative storytelling approaches and techniques in communicating science.

The videos were scored based on Quality of Storytelling (20%), Quality of Science Communication (30%), Quality of Public Health Message (10%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%), and our panel of expert judges selected the three winners of the Judges' Award. In addition, the general public voted for the Viewer's Choice Award.

Many thanks to the judges, students, teachers, parents, and voters who made this exciting competition happen!

Congratulations to the 2019 Winners:


Judges' Award First Place

The Criminal Case of the Aminoglycoside Misuser

By Brean Bognot and Cayla Tolentino of Mira Mesa High School, San Diego, CA
Team Advisor: Mrs. Lisa Yoneda



Judges' Award Second Place

The New Arms Race: Aminoglycoside Antibiotics

By Anvi Surapaneni and Vivian Hir of The Quarry Lane School, Dublin, CA
Team Advisor: Mrs. Alina Hamm



Judges' Award Third Place

The Three Little Bacteria and the Big Bad Tobramycin

By Carlos Hernandez, Jeff Huang, and Shamir Sheikh of Stuyvesant High School, New York, NY
Team Advisor: Mr. Gilbert Papagayo



Viewers' Choice Award

Mechanisms of Aminoglycoside Antibiotic Resistance

By Charumathi Badrinath of Rye Country Day School, Rye, NY
Team Advisor: Mrs. Jennifer Doran





2019 Challenge Details

In this challenge, students were asked to tell a story that communicating 2 things:

  1. The molecular changes that occur in bacteria that help them to become resistant to aminoglycoside antibiotics using relevant 3D protein structures.

    Videos were required to include a general introduction the biological function of ribosomes, a short description of how antibiotics affect the ribosomes, and a segment devoted to one of the aspects of the bacterial resistance:

    • Inactivation of the antibiotics via aminoglycoside modifying enzymes
    • Modifications of ribosomes by methyltransferases
    • Extraction of antibiotics from the bacterial cells via multidrug resistant efflux pumps
  2. The dangerously high level of antibiotic resistance caused by misuse and overuse of antibiotics. Students were required to explain how viewers might be affected, and what they can do prevent it.

The section below was avialable to the participants as introduction to the topic, and offred links to relevant 3D structures and additional resources.


Learn about the action of aminoglycoside antibiotics and the mechanisms of resistance

I. What are antibiotics?

Antibiotics are small molecules, originally discovered as defensive molecules made by fungi and other organisms, and now created by medical scientists. They bind to essential bacterial molecules, such as enzymes and ribosomes, blocking the growth of the bacteria or killing them. Because these bacterial proteins are structurally different from their animal equivalents or are non-existent in them, they cause no harm to the organism treated for bacterial infection.

Figure 1 presents main classes of antibiotics and their target protein/molecule organized by the biochemical process that they interrupt in bacteria. In this video challenge, we will be focusing only on the action of and resistance to the aminoglycoside class.

Figure 1

Main classes of antibiotics and their target protein/molecule organized by the biochemical process that they interrupt in bacteria. Download as PDF


II. How aminoglycoside antibiotics work

The aminoglycoside antibiotics are made by some bacteria to protect themselves from competing bacteria. They are particularly effective because they are very specific: they attack bacterial ribosomes, corrupting protein synthesis in the bacterium, but they don't attack the ribosomes of many other organisms, including our own ribosomes.

Ribosomes are the molecular machines that build new proteins based on the genetic information carried in the messenger RNA. Ribosomes are made up of multiple protein chains and rRNA that form the small and the large subunits. To learn more about the ribosomal subunits, read the Molecule of the Month on the topic.

Figure 2 shows eukaryotic and bacterial ribosomes drawn to scale and highlights the key differences in the nomenclature of their key components.

Figure 2

Eukaryotic ribosomes; PDB ID 6ek0 and prokaryotic ribosomes; PDB ID 4v5d.


Figure 3

Location of the A, P, and E binding sites inside ribosomes. tRNAs are shown in yellow, the mRNA in red, the beginnings of the polypeptide chain in aqua. PDB ID 4v5d

Despite structural differences, the ribosome in bacteria and prokaryotes follow the same steps in protein synthesis. Once the messenger RNA and a special initiator tRNA (different for prokaryotes and eukaryotes) bind to the smaller subunit of ribosomes, both subunits come together, creating the enzymatic environment for creating new protein chains. The stages of protein synthesis are described in the Molecule of the Month on Ribosome.

The ribosomes have 3 binding sites for the tRNA: A (acceptor site), P (peptidyl site), and E (exit site). Figure 3 shows the locations of these sites inside the ribosomes. The A (acceptor site) site is where the a tRNA carrying a matching codon to mRNA binds. During this step, the ribosome uses several interactions to test this pairing, ensuring that the base pairing is correct. You can explore these interactions in 3D in the Exploring the Structure section, in the Molecule of the Month on Ribosome.

The aminoglycoside antibiotics bind at the A site and they interfere with the recognition of the the matching tRNA, ultimately leading to mistakes in building the new protein chains. You can explore the aminoglycoside binding site in 3D in the Exploring the Structure section of the Molecule of the Month on Aminoglycoside Antibiotics.

Another mode of action for the aminoglycoside antibiotics is binding to the large subunit of the ribosome and causing problems at the end of protein synthesis, blocking the recycling of ribosomes after they are finished making a protein. You can explore this process in the Structural Biology Highlights article Antibiotics and Ribosome Function.

Aminoglycoside antibiotics are used mainly to treat infections caused by gram-negative bacteria in a clinical setting.

Table 1: Examples of Aminoglycoside Antibiotics and PDB structures with the antibiotic bound

Antibiotics and core structure Description Example PDB structure with the antibiotic bound Visualization resources and tips Learning Resources

Streptomycin: SRY

  • Discovered in 1943
  • Commonly used to treat Tuberculosis
  • Given intramuscularly

1fjg
Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotics streptomycin, spectinomycin, and paromomycin

This structure shows the small subunit of the ribosomes (colored green in the Chimera session) with streptomycin (SRY - red) attached in the active site.

1fjg NGL view a

Chimera session (preview below)b

Molecule of the Month on Aminoglycoside Antibiotics


Featured System article Antibiotics and ribosome function


2018 calendar Mechanisms of Antimicrobial Resistance page for May

Gentamycin: LLL

  • Discovered in 1963
  • Active against a wide range of mostly Gram-negative bacteria including Pseudomonas, Proteus, Escherichia coli, Klebsiella pneumoniae, Enterobacter aerogenes, Serratia, and the Gram-positive Staphylococcus

4v53
Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin.

This structure shows the large and small ribosomal subunits (colored blue and green respectively in the Chimera session) with gentamycin (LLL - red) attached in the small subunit’s active site (interfering with the protein production) and in the large subunit’s active site (blocking the recycling of the ribosomes).

4v53 NGL view a

Chimera session (preview below)b

Tobramycin: TOY

  • Active against Pseudomonas aeruginosa
  • Given intravenously or intramuscularly; Inhalation Solution introduced in 2012 to treat lung infections associated with cystic fibrosis (CF)

4lfc
Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

This structure shows the small subunit of the ribosomes (colored green in the Chimera session) with tobramycin (TOY - red) attached in the active site.

4lfc NGL view a

Chimera session (preview below)b

III. Mechanisms of bacterial resistance to aminoglycoside antibiotics

In the face of overuse and misuse of antibiotics, new strains of bacteria have emerged that can proliferate even in the presence of the newest antibiotics. There are multiple ways the bacteria adapt to develop resistance against the aminoglycoside antibiotics. Of current clinical prominence are the following three molecular mechanisms:

  1. Aminoglycoside modifying enzymes
  2. Ribosomal methyltransferases
  3. Efflux pumps that remove the antibiotics from the bacterial cell

There are two ways in which the resistance genes for each of these mechanisms can be passed on: via Chromosome, where the gene is transferred from generation to generation (vertical transfer) and via a plasmid that can be passed from bacterial species to species (horizontal transfer).


1. Aminoglycoside modifying enzymes

Aminoglycoside modifying enzymes alter the structure of antibiotics directly so that they can’t attach to their target. They are a large family containing three subclasses based on the type of modification that they apply to the the antibiotic:

O-nucleotidyltransferase (ANT):
these enzymes add a nucleotide to the drug


Before Reaction: Tobramycin: TOY

After Reaction: Adenylated Tobramycin 51H

--------->


N-acetyltransferases (AAC):
these enzymes add an acetyl group to the antibiotic

Before Reaction: Gentamycin: LLL


After Reaction Acetylated Gentamicin 8MM

------>


O-phosphotransferase (APH):
these enzymes connect a phosphate to the drug



Table 2: Example PDB entries for aminoglycoside modifying enzymes


Example PDB structure

Expressing Gene

Visualization hints and resources

Learning resources

O-nucleotydyltransferase (ANT):


Before Reaction:
5cfs
Crystal Structure of ANT(2")-Ia in complex with AMPCPP and tobramycin


After Reaction:
5cfu
Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin

aadB


PDB entries 5cfs and 5cfu (colored blue in the Chimera session) show the enzyme before and after the reaction. Tobramycin is orange. In the “before” structure, a non-reactive analog of ATP (yellow) is used to freeze the reaction, and in the second structure, the nucleotide (colored lighter orange) has been attached to the antibiotic.

Chimera session (preview below)b


5fcs NGL view a

5fcu NGL view a

Molecule of the Month on Aminoglycoside Antibiotics and Resistance


Molecule of the Month on Aminoglycoside Antibiotics


2018 calendar Mechanisms of Antimicrobial Resistance page for June

Superbugs! How Bacteria Evolve Resistance to Antibiotics Poster

N-acetyltransferases (AAC):

1bo4
Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase.


aacC1

The structure contains 2 subunits (colored shades of blue in the Chimera session). Each subunit has coenzyme A (COA - yellow) bound in the active site. Spermidine (SPD - orange) is bound in the gentamicin-binding site.

Chimera session (preview below)b


1bo4 NGL view a


O-phosphotransferase

1l8t

Crystal Structure Of 3',5"-Aminoglycoside Phosphotransferase Type IIIa ADP Kanamycin A Complex

aphA

Aminoglycoside Phosphotransferase (colored blue in the Chimera session) is bound to Kanamycin (KAN – Orange) and ADP (yellow). The phosphate group colored darker yellow will be attached to Kanamycin during the reaction.

Chimera session (preview below)b


1l8t NGL view a


2. Ribosomal methyltransferases

The ribosomal methyltransferases modify ribosomes enzymatically by adding methyl groups to a nucleotide on the 16S rRNA in the aminoglycoside binding site. This does not affect the function of the ribosome, but prevents the antibiotic from binding.

Table 3: Example PDB structures for ribosomal methytransferases


Example PDB structure

Expressing Gene

Visualization hints and resources

Learning resources

4ox9
Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

npmA

The structure shows small ribosomal subunit (colored green in the Chimera session) with the methyltransferase enzyme (Chain Y - magenta) bound to it. The key nucleotide (Adenine 1408) that the enzyme will add methyl group to in the course of the reaction is highlighted in lighter green.

Chimera session (preview below)b


4ox9 NGL view a

Molecule of the Month on Aminoglycoside Antibiotics and Resistance


Molecule of the Month on Aminoglycoside Antibiotics

Superbugs! How Bacteria Evolve Resistance to Antibiotics Poster

3frh
Structure of the 16S rRNA methylase RmtB, P21

rmtB

The structure shows the methyltransferase enzyme (colored magenta in the Chimera session) with S-adenosyl-L-homocysteine (SAH - green) bound in the active site. The S-adenosyl-L-homocysteine has a great structural similarity to S-Adenosyl methionine, the molecule that the enzyme normally uses to extract the methyl group from and add it to the nucleotide on the rRNA.

Chimera session (preview below)b


3frh NGL view a


3. Efflux pumps that remove the antibiotics from the bacterial cell

Multidrug resistance transporters or efflux pumps find drugs that try to gain entry through a cell membrane and they transport them back outside.

Bacteria possess multidrug resistance (MDR) gene regulators that can sense when the antibiotics get into the bacterial cell, and prompt the synthesis of the multidrug resistance pumps to eject them.

Table 4: Example of efflux pump and a multidrug resistance (MDR) gene regulator


Example PDB structure

Expressing Gene

Visualization hints and resources

Learning resources

Gram-negative bacteria multidrug efflux pump:

5o66
Asymmetric AcrABZ-TolC

tolC, acrA, acrB, acrZ

The structure shows an efflux pump from Gram-negative bacteria. For your reference, the inner and outer membranes are highlighted on the Chimera session preview.

Chimera session (preview below)b


5o66 NGL view a

Molecule of the Month on Multidrug Resistance Transporters


2018 calendar "Mechanisms of Antimicrobial Resistance" pages for November and December

Superbugs! How Bacteria Evolve Resistance to Antibiotics Poster

Multidrug resistance (MDR) gene regulator

3q3d
Crystal structure of BmrR bound to puromycin

bmrR

The structure shows a fragment of bacterial DNA (colored yellow on the Chimera session) with the gene regulator bound to it. The gene regulator has puromycin (orange) bound in each subunit.

Chimera session (preview below)b


3q3d NGL view a



Visualization Resources

  1. The user guide for NGL can be found here. The NGL is the default 3D viewer accessible from each structure summary page, from the tab “3D View”.
  2. You can download and open these sessions using UCSF Chimera. Use the tutorials available here and here to edit the sessions, create animations or save pictures.

References

  1. Sylvie Garneau-Tsodikovaa and Kristin J. Labby (2016) Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives. Medchemcomm. 7(1): 11–27.

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