Proteopedia - User contributions [en]

Ribosome

2020-11-05T17:50:18Z

Margaret Franzen: added categories

<StructureSection load='4v42' size='450' side='right' scene='User:Wayne_Decatur/SandboxRibosome/Bothmodels6/1' caption='The Ribosome ([[4v42]])'>
__TOC__
==Introduction==
The [http://en.wikipedia.org/wiki/ribosome ribosome] is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as [http://sandwalk.blogspot.com/2009/10/ribosome-and-central-dogma-of-molecular.html the Central Dogma of Molecular Biology]. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains.

==Nobel Prize Winners and Other Contributors==
Venkatraman Ramakrishnan of the M.R.C. Laboratory of Molecular Biology in Cambridge, England; Thomas A. Steitz of Yale University; and Ada E. Yonath of the Weizmann Institute of Science in Rehovot, Israel have been awarded the [http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ the 2009 Nobel Prize in Chemistry]<ref>[[Nobel Prizes for 3D Molecular Structure]].</ref> for their landmark work revealing the atomic details of the molecular machine that make proteins in all cells, [http://en.wikipedia.org/wiki/ribosome the ribosome]. Their findings are the gloriously enlightening culmination of years of work<ref>PMID: 19833925</ref>, first heralded by Ada Yonath's report of crystals in 1980<ref>Yonath A, Mussig J, Tesche B, Lorenz S, Erdmann VA, Wittmann HG. Crystallization of the large ribosomal subunits from Bacillus stearothermophilus. Biochem. Internat. 1980 1:428-435.</ref>. Others made significant contributions to the detailed structure of this machine, as poignantly summarized by [https://loop.nigms.nih.gov/index.php/2009/10/07/2009-chemistry-nobel-prize-recognizes-the-determination-of-the-ribosomes-three-dimensional-structure/ Jeremy Berg, current Director of National Institute of General Medical Sciences, in his announcement]
<blockquote>
The Nobel committee has the daunting challenge of limiting itself to up to three laureates for each prize. Several other long-time NIGMS grantees who also contributed greatly to our understanding of the structure and function of the ribosome include Peter Moore, Harry Noller and Joachim Frank.
</blockquote>
The American Society for Biochemistry and Molecular Biology posted [http://www.asbmb.org/News.aspx?id=3612 an announcement of the prize echoing this sentiment] as well.

==Impact of Ribosome Structure==
The ribosome ranks among the [[Highest impact structures|known structures with highest impact]]. Imagine the wonder and thrill at suddenly knowing how tens of proteins and large and small RNAs fit together into the elegant machines that serve as the protein factories in every cell and organelle of every organism on the planet. The immense size of the ribosome and each of the two individual ribosomal subunits that come together to form the complete ribosome that is active in translation made for a daunting task in structure determination. '''These structures were at the time they were first determined, and remain (in 2009), the largest asymmetric molecules solved crystallographically.''' In addition to providing us immense insight into the general molecular and atomic details of protein synthesis in every organism on earth, the development of new antibiotics are likely to rely on this ground-breaking work.

==Ribosome Components==
 
·· {{Link Toggle 70SribotRNAs}} ·· {{Link Toggle 70SribomRNA}} ·· {{Link Toggle 70SriborRNA}} ·· {{Link Toggle 70SriboProtein}} ·· {{Link Toggle 70SriboAsitetRNA}} ·· {{Link Toggle 70SriboPsitetRNA}} ·· {{Link Toggle 70SriboEsitetRNA}} ·· {{Link Toggle 70SriboLSU}} ·· {{Link Toggle 70SriboSSU}} ·· {{Link Toggle BlackWhiteBackground}} ··

The small subunit of the prokaryotic ribosome sediments at 30S<ref>[http://en.wikipedia.org/wiki/Svedberg Svedberg unit] in Wikipedia</ref>. It is composed of a 16S chain of RNA about 1,500 bases long (~500 kDa), plus about 20 protein chains. The proteins in the first small subunit determined range from about 3 kDa to 29 kDa.

The large subunit of the prokaryotic ribosome sediments at 50S. It is composed of two chains of RNA, a 23S chain (~3000 bases long, 946 kDa) and a 5S chain (~120 bases long, 39 kDa). Assembled with the RNA are about 30 protein chains. The proteins in the first large subunit determined range from 6 kDa to 37 kDa. See also [[Large Ribosomal Subunit of Haloarcula]]. The large subunit contains several [[Kink-turn motif]]s.

The ''mitochindrial ribosome'' or '''mitoribosome''' is smaller than the the cytoplasmic ribosome with a small subunit which sediments at 28S and a large subunit which sediments at 39S. The whole mitoribosome sediments at 55S.

Other macromolecules in a functioning ribosome include three transfer RNA molecules, messenger RNA, and the nascent protein chain.

Thus, a complete functioning prokaryotic ribosome contains 7 RNA chains (including three tRNA's and one mRNA), 47 ribosomal protein chains, and one nascent protein chain. The total molecular mass is several million daltons.

The cytoplasmic ribosomes of eukaryotes are larger with more RNA and proteins. Eukaryotic cytoplasmic ribosomes also have an additional RNA in the large subunit, the 5.8S rRNA, that is about 150 nts and related to the 5' end of prokaryotic rRNA. In regards to the size, the ribosomal subunits of budding yeast and humans sediment at 40S and 60S; the complete ribosome sediments at 80S and it is generally about another million daltons larger than the prokaryotic one.

==The Peptidyl Transferase Is A Ribozyme==
The small subunit of the ribosome is the main site of decoding, directing the interaction of the messenger RNA codon with the anticodon stem-loops of the proper transfer RNA. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked. However, it is important to keep in mind that in the active ribosome the two subunits are in contact via bridges, and the actions in one subunit affect the other as the process of translation advances through the stages of initiation, elongation, and termination.

The initial determination of the atomic resolution structures of the subunits '''surprisingly revealed that RNA, but not protein, contributes directly to forming the site of both decoding and catalysis of peptide bond synthesis, with the ribosomal proteins only acting in an ancillary role''', see [[ribozyme]]. (Examine the structural data concerning peptide bond synthesis [[Large Ribosomal Subunit of Haloarcula#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|here]].) During the elongation stage of translation, new peptides are added to the carboxy-terminus of the growing nascent chain that is linked to the acceptor-end of the tRNA in the peptidyl or P site. As the nascent chain grows, it advances into a tunnel that passes through the large subunit, called the polypeptide exit tunnel. Several factors can interact at the site of extrusion of the nascent polypeptide chain to ensure proper folding or transport across a membrane. Additionally, during protein synthesis, many additional factors such as elongation factors (EF-Tu and EF-G) interact with the ribosome to elicit decoding and peptide bond synthesis accurately and efficiently. Structures of several of these factors in complex with the ribosome, as well as intermediate states in the process, are being observed now, building upon the first atomic structures.

==First Atomic-Resolution Ribosome Structures==
The particular structures for which the Nobel prize was awarded were published in 2000 and were subsequently refined or improved upon. All these structures were determined using proteins from [[extremophiles]]. Here are the links to the Proteopedia entries:

*Yonath lab original atomic-resolution structures<ref>PMID: 11007480</ref><ref>PMID: 11733066</ref>: Thermus thermophilus small ribosomal subunit - [[1fka]], improved in [[1i94]], [[1i95]], [[1i96]], and [[1i97]]. Thermus thermophilus is a [[Extremophiles|thermophilic]] eubacteria. Deinococcus radiodurans large ribosomal subunit - [[1nkw]], later refined to give [[2zjr]]. Deinococcus radiodurans is a mesophilic eubacteria. 

*Ramakrishnan lab original atomic-resolution structures<ref>PMID: 11014182</ref><ref>PMID: 11014183</ref>: Thermus thermophilus small ribosomal subunit in [[1j5e]]. Related: in complex with the antibiotics streptomycin, spectinomycin, and paromomycin in [[1fjg]]; in complex with tetracycline in [[1hnw]], pactamycin in [[1hnx]], hygromycin B in [[1hnz]].
The Thermus thermophilus small ribosomal subunit is composed of a 16S chain of RNA about 1,522 bases long (494 kDa), plus 20 protein chains (S2-S20, THX). The protein chains range from 26 (THX, 3 kDa) to 256 amino acids (S2, 29 kDa).

*Steitz and Moore labs original atomic-resolution structures<ref>PMID:10937989</ref><ref>PMID: 10937990</ref>: Haloarcula marismortui large ribosomal subunit - [[1ffk]] and later refined to give [[1jj2]], and then refined to give [[1s72]], and later [[3cc2]]<ref>PMID:18455733</ref>. Related: [[1ffz]], [[1fg0]]. Haloracula is a [[Extremophiles|halophilic]] archaea. Assembled with the ribosomal RNAs (2,922 and 122 nucleotides long) in the structure are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa).<ref>PMID:10937989</ref>

==Proteopedia Topic Pages Covering the Ribosome and Subunits==
*[[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] as solved by the Steitz & Moore labs. 
*[[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome|Interactions between Antibiotics and the Ribosome]] 
*[[Large Ribosomal Subunit of Haloarcula]] 
*[[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|Azithromycin bound to the Large Ribosomal Subunit of Haloarcula marismortui]] 
*[[40S rRNA and proteins and P/E tRNA for eukaryotic ribosome]] 
*[[Ribosomal A Site Binding Paromomycin: A Morph]] 
*[[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] 
*[[Ribosome structure]] 
*[[Ribosome structure (Spanish)]] 
*[[Ribosome (Czech)]] 

==Ribosome 3D structures==

[[Ribosome 3D structures]]

==See Also==

* [[Nobel Prizes for 3D Molecular Structure]]
* [[Highest impact structures]] of all time
* [[Translation]]
* [[DNA Replication, Transcription and Translation]]
* [[tRNA]]
* [[LepA|Escherichia coli LepA, the ribosomal back translocase]]
* [[Extremophiles]]
* [[RNA]]
* [[Ribozyme]]
* For Spanish see [[Ribosoma 70S]]

==References==
<references />

==Additional Literature and Resources==
<ref group="xtra">PMID:19222865</ref><ref group="xtra">PMID: 19838167</ref><ref group="xtra">PMID: 11297922</ref><ref group="xtra">PMID: 19962317</ref><ref group="xtra">PMID: 19938030</ref><ref group="xtra">PMID: 18547810</ref><ref group="xtra">PMID: 17764954</ref><ref group="xtra">PMID: 18292779</ref><ref group="xtra">PMID: 19089882</ref><ref group="xtra">PMID: 23771137</ref><references group="xtra"/>
*[http://apollo.chemistry.gatech.edu/RiboVision/ RiboVision] - a nice way to explore the representative structures with the secondary structures of the RNA side-by-side with the 3D structure, from from Georgia Institute of Technology and NASA.
*The people behind [http://apollo.chemistry.gatech.edu/RiboVision/ RiboVision] have determined a [http://nar.oxfordjournals.org/content/41/15/7522.short?rss=1 revised secondary structure for two of the rRNAs] based on the 3D structures and it is described in [http://www.ncbi.nlm.nih.gov/pubmed/23771137?dopt=Abstract their paper]<ref group="xtra">PMID: 23771137</ref>.
*[http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/news/news_2009.html#20091013 RCSB Protein Data Bank coverage of the 2009 Nobel Prizes in Chemistry]
*[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb121_1.html 70S Ribosome: January 2010 Molecule of the Month] as part of the series of tutorials that are at [http://www.pdb.org/pdb/home/home.do the RCSB Protein Data Bank] and written by [[User:David_S._Goodsell|David Goodsell]]
*[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb10_1.html Ribosome: October 2000 Molecule of the Month] as part of the series of tutorials that are at [http://www.pdb.org/pdb/home/home.do the RCSB Protein Data Bank] and written by [[User:David_S._Goodsell|David Goodsell]]

[[Category:Topic Page]]
[[Category:Translation]]
[[Category:Ribosome]]
[[Category: BioMolViz]]
[[Category: Macromolecular Assemblies]]

Backbone representations

2020-11-05T17:45:10Z

Margaret Franzen: added categories

Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer [[chain]] structure to be seen. In proteins, a simple  backbone trace  connects alpha carbons (shown as '''balls''' in the <scene name='59/599354/Helix/13'>initial scene</scene>) but the  backbone trace line  does not coincide with any of the covalent bonds in the main chain.

<StructureSection load='' size='450' side='right' caption='' scene='59/599354/Helix/13'>
==Protein Main Chain==

Lets begin with <scene name='59/599354/Helix/1'>all atoms of a small alpha helix</scene> (15 amino acids)<ref>Residues 23-37 from [[1pgb]].</ref> The atoms and bonds are colored by element:
{{Template:ColorKey_Element_C}}
{{Template:ColorKey_Element_H}}
{{Template:ColorKey_Element_O}}
{{Template:ColorKey_Element_N}}.

*First, we'll simplify by <scene name='59/599354/Helix/2'>hiding the hydrogen atoms</scene>. [[Hydrogen in macromolecular models|Hydrogen]] atoms make up almost exactly 50% of the atoms in proteins.

*Next, we'll simplify by <scene name='59/599354/Helix/3'>hiding the amino acid side chains</scene>. What remains is called the main chain. Each amino acid's main chain atoms are N-C-C, where the first C is the '''alpha carbon (shown as a ball)''', and the second, the carboxyl carbon with its double-bonded oxygen (double bonds not shown). We could also <scene name='59/599354/Helix/4'>hide the oxygen atoms</scene>, leaving only the atoms that are part of the '''main chain''', also called the backbone.

==Protein Backbone Trace==

<scene name='59/599354/Helix/5'>Backbone Trace</scene>: Now we'll draw a  yellow line  between alpha carbons (balls). This line is called a  backbone trace . Note that the backbone trace does not follow any actual covalent chemical bonds -- it simply
connects alpha carbon positions, thereby simplifying the representation.

*<scene name='59/599354/Helix/6'>Hiding all atoms except alpha carbons</scene> makes the backbone trace even clearer.

*Here is the <scene name='59/599354/Helix/7'>backbone trace by itself</scene>.

==Smoothed Protein Backbone Trace==

A <scene name='59/599354/Helix/8'>smoothed backbone trace</scene> is another common backbone representation. Here, the  smoothed backbone trace is green .

*Here is the <scene name='59/599354/Helix/9'>smoothed backbone trace alone</scene>.

==Ribbon Backbone Trace==

Perhaps the most common protein backbone representation is the <scene name='59/599354/Helix/10'>ribbon</scene>. Here the  ribbon is violet , the [[DRuMS#Element|standard secondary structure color]] for alpha helices. As you can see, the ribbon is a smoothed backbone trace expanded in width. The''' arrowhead''' at one end points to the carboxyl terminus.

*Here is the <scene name='59/599354/Helix/11'>ribbon alone</scene>.

*Here the <scene name='59/599354/Helix/12'>ribbon is decorated with sticks representing all atoms in this helix</scene>.

==Protein Domain Example==
Now lets look at a <scene name='59/599354/Domain/1'>small protein domain</scene> ([[1pgb]]). This domain contains the alpha helix used above, but also contains a small beta sheet made of four beta strands, plus loops (regions that are neither alpha helix nor beta strand) connecting the helices and strands. The helices and strands are represented as ribbons, while the "ropes" connecting them are smoothed backbone traces. This type of representation is properly called a '''secondary structure schematic''', but is called a '''cartoon''' in [[Jmol]] and its family of ancestral visualization programs ([[RasMol]], [[Chime]]). '''Arrowheads''' point towards the carboxy terminus.

*A <scene name='59/599354/Domain/10'>useful way of coloring</scene> such a ribbon representation is with a spectral sequence of colors from the amino (N) terminus to the carboxy (C) terminus. (Proteins are synthesized by adding amino acids to the C terminus.) This color scheme is called '''N->C Rainbow'''. Notice how the arrowheads point towards the C terminus.
{{Template:ColorKey_N2CRainbow}}

*Next, lets <scene name='59/599354/Domain/2'>color by secondary structure</scene>:
{{Template:ColorKey_Helix}},
{{Template:ColorKey_Strand}},
{{Template:ColorKey_Loop}}.

*For comparison, here are <scene name='59/599354/Domain/9'>all the atoms in this domain</scene>.

*Here are the <scene name='59/599354/Domain/4'>atoms alone</scene>, without the ribbon.

*A simple <scene name='59/599354/Domain/5'>backbone</scene> for this small domain.

*The domain <scene name='59/599354/Domain/6'>backbone plus the smoothed backbone trace</scene>.

*The <scene name='59/599354/Domain/7'>smoothed backbone trace alone</scene>.

</StructureSection>

== See Also ==
*[[Introduction to molecular visualization]]
*[[Secondary structure]] which has links to other pages with details on alpha helices, beta sheets, and turns.
== References ==
<references/>
[[Category: BioMolViz]]
[[Category: Alternate Renderings]]

Category:Alternate Renderings

2020-11-05T17:44:33Z

Margaret Franzen:

Alternate Renderings is one of twelve overarching themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project].

'''Overarching theme'''

Alternate Renderings (AR) ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Learning Goals:'''

''' AR1.''' Students can create meaningful molecular images to convey features such as secondary structure, cpk coloring, active sites and molecular interactions.

'''AR2.''' Students can produce the best rendering of a macromolecule to use in a given situation.

Category:Topology and Connectivity

2020-11-05T17:39:33Z

Margaret Franzen:

Topology and Connectivity (TC) is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Topology and Connectivity (TC) ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

'''Learning Goals'''

'''TC1.''' Students can describe the linkages between building blocks within a macromolecule.

'''TC2.''' Students can describe the overall shape and common motifs within a 3D macromolecular structure.

'''TC3.''' Students can explain how any given biomolecular interaction site can be made by a variety of topologies.

Category:Symmetry/Asymmetry Recognition

2020-11-05T17:38:35Z

Margaret Franzen:

Symmetry/Asymmetry Recognition is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Symmetry/Asymmetry Recognition (SA) ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

'''Learning Goals:'''

'''SA1.''' Students can identify symmetric or asymmetric features in rendered molecules.

'''SA2.''' Students can hypothesize the functional significance of symmetry or asymmetry in rendered molecules.

Category:Structure‐Function Relationship

2020-11-05T17:37:37Z

Margaret Franzen:

Structure‐Function Relationship is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Structure‐Function Relationship (SF) ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

'''Learning Goals:'''

'''SF1.''' Students can evaluate biomolecular interaction sites using molecular visualization tools.

'''SF2.''' Using molecular visualization, students can predict the function of biomolecules.

'''SF3.''' Using molecular visualization, students can predict the function of an altered macromolecule.

Category:Structural Model Skepticism

2020-11-05T17:36:24Z

Margaret Franzen:

Structural Model Skepticism is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Structural Model Skepticism (SK) ‐ Recognition of the limitations of models to describe the structure of macromolecules.

'''Learning Goals:'''

'''SK1.''' Students can critique the limitations of a structural model of a macromolecule.

'''SK2.''' Students can evaluate the quality of 3D models including features that are open to alternate interpretations based on molecular visualization and PDB flat files.

'''SK3.''' Students can discuss the value of experimentally altering a biomolecule to facilitate structure determination.

Category:Molecular Interactions

2020-11-05T17:35:15Z

Margaret Franzen:

Molecular Interactions is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Molecular Interactions (MI) ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Learning Goals: '''

'''MI1.''' Students can predict the existence of an interaction using structural information (e.g. bond lengths).

'''MI2.''' Students can evaluate the effect of the local environment on various molecular interactions.

Category:Molecular Interactions

2020-11-05T17:35:02Z

Margaret Franzen:

Molecular Interactions is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Molecular Interactions (MI) ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Learning Goals: '''
'''MI1.''' Students can predict the existence of an interaction using structural information (e.g. bond lengths).

'''MI2.''' Students can evaluate the effect of the local environment on various molecular interactions.

Category:Molecular Dynamics

2020-11-05T17:34:05Z

Margaret Franzen:

Molecular Dynamics is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Molecular Dynamics (MD) ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Learning Goals:'''

'''MD1.''' Students can describe the impact of the dynamic motion of a biomolecule on its function.

'''MD2.''' Students can predict limits to macromolecular movement.

Category:Molecular Dynamics

2020-11-05T17:33:50Z

Margaret Franzen:

Molecular Dynamics is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Molecular Dynamics (MD) ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Learning Goals:'''
'''MD1.''' Students can describe the impact of the dynamic motion of a biomolecule on its function.

'''MD2.''' Students can predict limits to macromolecular movement.

Category:Macromolecular Building Blocks

2020-11-05T17:32:57Z

Margaret Franzen:

Macromolecular Building Blocks is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Macromolecular Building Blocks (MB) ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

'''Learning Goals:'''

'''MB1.''' Students can identify individual building blocks of biological polymers.

'''MB2.''' Students can describe the contributions different individual building blocks make in determining the 3‐D shape of the polymer.

Category:Macromolecular Assemblies

2020-11-05T17:31:51Z

Margaret Franzen:

Macromolecular Assemblies is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Macromolecular Assemblies (MA) ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

'''Learning Goals:'''

'''MA1.''' Students can describe various macromolecular assemblies.

'''MA2.''' Students can compose information‐rich renderings of macromolecular assemblies.

Category:Ligands and Modifications

2020-11-05T17:30:57Z

Margaret Franzen:

Ligands and Modifications is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Ligands and Modifications (LM) ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

'''Learning Goals:'''

'''LM1.''' Students can identify ligands and modified building blocks within a rendered structure.

'''LM2.''' Students can describe the impact of a ligand or modified building block on the structure/function of a macromolecule.

Category:Construction and Annotation

2020-11-05T17:29:03Z

Margaret Franzen:

Construction and Annotatiion s one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Construction and Annotation (CA) ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

'''Learning Goals:'''

'''CA1.''' Students can compose information‐rich renderings of macromolecule‐ligand interactions.

'''CA2.''' Students can predict the cellular location/function of a protein based on the positions of polar and nonpolar residues.

Category:Alternate Renderings

2020-11-05T17:27:37Z

Margaret Franzen:

Alternate Renderings is one of twelve Overarching Themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. This work is part of [https://biomolviz.org/ BioMolViz Project], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Theme'''

Alternate Renderings (AR) ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Learning Goals:'''

'''AR1.''' Students can create meaningful molecular images to convey features such as secondary structure, cpk coloring, active sites and molecular interactions.

'''AR2.''' Students can produce the best rendering of a macromolecule to use in a given situation.

Category:Atomic Geometry

2020-11-05T17:25:56Z

Margaret Franzen:

Atomic Geometry is one of twelve overarching themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. More information about the BioMolViz project can be found at: https://biomolviz.org/], with additional information [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching theme'''

Atomic Geometry (AG): three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Learning Goals:'''

'''AG1. '''Students can describe the ideal geometry for a given atom within a molecule and deviations from the ideal geometry due to neighboring interactions.

'''AG2.''' Students can compare and contrast different structural conformations with regard to energy, addition of substituents, and impact on structure/function of a macromolecule.

'''AG3.''' Students can describe the effect of dihedral/torsion angles on macromolecular structure.

Category:BioMolViz

2020-11-05T17:24:30Z

Margaret Franzen:

The goal of the BioMolecular Visualization Group (BioMolViz) is to promote molecular visualization literacy. This group of educators, assessment experts and biomolecular visualization enthusiasts began in 2012 to expand the Biomolecular Visualization Framework (Bateman and Craig 2010). The expanded Framework includes twelve ‘Overarching Themes’ (listed below), which are further expanded into learning goals and learning objectives (Dries et al. 2016). The group is currently developing a repository of assessments to measure molecular visualization literacy and welcomes input and engagement from the broader community. More information can be found on the [https://biomolviz.org/ BioMolViz website] and [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here].

'''Overarching Themes in the BioMolViz Framework:'''

'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Alternate Renderings (AR)''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Construction and Annotation (CA)''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

'''Ligands and Modifications (LM)''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

'''Macromolecular Assemblies (MA)''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

'''Macromolecular Building Blocks (MB)''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

'''Molecular Dynamics (MD)''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Molecular Interactions (MI)''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Structural Model Skepticism (SK)''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.

'''Structure‐Function Relationship (SF)''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

'''Symmetry/Asymmetry Recognition (SA)''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

'''Topology and Connectivity (TC)''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

'''References:'''

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.

Category:BioMolViz

2020-11-05T17:23:47Z

Margaret Franzen:

The goal of the BioMolecular Visualization Group (BioMolViz) is to promote molecular visualization literacy. This group of educators, assessment experts and biomolecular visualization enthusiasts began in 2012 to expand the Biomolecular Visualization Framework (Bateman and Craig 2010). The expanded Framework includes twelve ‘Overarching Themes’ (listed below), which are further expanded into learning goals and learning objectives (Dries et al. 2016). The group is currently developing a repository of assessments to measure molecular visualization literacy and welcomes input and engagement from the broader community. More information can be found on the [https://biomolviz.org/ BioMolViz website] and [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here]..

'''Overarching Themes in the BioMolViz Framework:'''

'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Alternate Renderings (AR)''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Construction and Annotation (CA)''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

'''Ligands and Modifications (LM)''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

'''Macromolecular Assemblies (MA)''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

'''Macromolecular Building Blocks (MB)''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

'''Molecular Dynamics (MD)''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Molecular Interactions (MI)''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Structural Model Skepticism (SK)''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.

'''Structure‐Function Relationship (SF)''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

'''Symmetry/Asymmetry Recognition (SA)''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

'''Topology and Connectivity (TC)''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

'''References:'''

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.

Category:BioMolViz

2020-11-05T17:23:26Z

Margaret Franzen:

The goal of the BioMolecular Visualization Group (BioMolViz) is to promote molecular visualization literacy. This group of educators, assessment experts and biomolecular visualization enthusiasts began in 2012 to expand the Biomolecular Visualization Framework (Bateman and Craig 2010). The expanded Framework includes twelve ‘Overarching Themes’ (listed below), which are further expanded into learning goals and learning objectives (Dries et al. 2016). The group is currently developing a repository of assessments to measure molecular visualization literacy and welcomes input and engagement from the broader community. More information can be found on the [https://biomolviz.org/ BioMolViz website] and [http://proteopedia.org/wiki/index.php/Kristen_Procko/BioMolViz here]..

'''Overarching Themes in the BioMolViz Framework:'''

'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Alternate Renderings (AR)''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Construction and Annotation (CA)''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

'''Ligands and Modifications (LM)''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

'''Macromolecular Assemblies (MA)''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

'''Macromolecular Building Blocks (MB)''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

'''Molecular Dynamics (MD)''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Molecular Interactions (MI)''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Structural Model Skepticism (SK)''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.

'''Structure‐Function Relationship (SF)''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

'''Symmetry/Asymmetry Recognition (SA)''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

'''Topology and Connectivity (TC)''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

'''References:'''

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.

Category:Atomic Geometry

2020-11-05T17:08:12Z

Margaret Franzen:

Atomic Geometry is one of twelve overarching themes in the Biomolecular Visualization (BioMolViz) Framework. The Framework identifies learning goals to assist in developing biomolecular visualization literacy. More information about the BioMolViz project can be found at: https://biomolviz.org/.

'''Overarching theme'''

Atomic Geometry (AG): three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Learning Goals:'''

'''AG1. '''Students can describe the ideal geometry for a given atom within a molecule and deviations from the ideal geometry due to neighboring interactions.

'''AG2.''' Students can compare and contrast different structural conformations with regard to energy, addition of substituents, and impact on structure/function of a macromolecule.

'''AG3.''' Students can describe the effect of dihedral/torsion angles on macromolecular structure.

Category:BioMolViz

2020-11-05T17:05:54Z

Margaret Franzen:

The goal of the BioMolecular Visualization Group (BioMolViz) is to promote molecular visualization literacy. This group of educators, assessment experts and biomolecular visualization enthusiasts began in 2012 to expand the Biomolecular Visualization Framework (Bateman and Craig 2010). The expanded Framework includes twelve ‘Overarching Themes’ (listed below), which are further expanded into learning goals and learning objectives (Dries et al. 2016). The group is currently developing a repository of assessments to measure molecular visualization literacy and welcomes input and engagement from the broader community. More information can be found on the [https://biomolviz.org/ BioMolViz website].

'''Overarching Themes in the BioMolViz Framework:'''

'''Atomic Geometry (AG)''' ‐ three‐atom and four‐atom dihedral/torsion angles, metal size and metal‐ligand geometries, steric clashes.

'''Alternate Renderings (AR)''' ‐ Rendering of a macromolecular structure such as a protein or nucleic acid structure in various ways from the simplest possible way (connections between alpha carbons) to illustration of secondary structure (ribbons) to surface rendering and space filling.

'''Construction and Annotation (CA)''' ‐ Ability to build macromolecular models, either physical or computerized, and, where possible, add commentary, either written or verbal, to tell a molecular story.

'''Ligands and Modifications (LM)''' ‐ Metals and metal clusters, additions such as glycosylation, phosphorylation, lipid attachment, methylation etc.

'''Macromolecular Assemblies (MA)''' ‐ Polypeptides, oligosaccharides, and nucleic acid and lipid superstructures.

'''Macromolecular Building Blocks (MB)''' ‐ Recognition of native amino acids, nucleotides, sugars, and other biomonomer units/building blocks. Understanding of their physical and chemical properties, particularly regarding functional groups.

'''Molecular Dynamics (MD)''' ‐ Animated motion simulating conformational changes involved in ligand binding or catalysis, or other molecular motion/dynamics.

'''Molecular Interactions (MI)''' ‐ Covalent and noncovalent bonding governing ligand binding and subunit‐subunit interactions.

'''Structural Model Skepticism (SK)''' ‐ Recognition of the limitations of models to describe the structure of macromolecules.

'''Structure‐Function Relationship (SF)''' ‐ Active/binding sites, microenvironments, nucleophiles, redox centers, etc.

'''Symmetry/Asymmetry Recognition (SA)''' ‐ Recognition of symmetry elements within both single chain and oligomeric macromolecules.

'''Topology and Connectivity (TC)''' ‐ Following the chain direction through the molecule, translating between 2D topology mapping and 3D rendering.

'''References:'''

Bateman, Robert C., and Paul A. Craig. 2010. “Education Corner: A Proficiency Rubric for Biomacromolecular 3D Literacy.” PDB Newsletter 45: 5–7.

Dries, Daniel R., Diane M. Dean, Laura L. Listenberger, Walter R.P. Novak, Margaret A. Franzen, and Paul A. Craig. 2016. “An Expanded Framework for Biomolecular Visualization in the Classroom: Learning Goals and Competencies.” Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.20991.