Proteopedia - User contributions [en]

Christopher Berndsen/Proteopedia

2017-08-07T13:38:19Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Students then present their pages to the class as an oral presentation.

'''2017 Proteopedia Projects'''
----
[[Avelox_%28moxifloxacin%29|Avelox]]

[[Cancidas|Cancidas]]

[[Diuril|Diuril]]

[[Follistin|Follistin]]

[[Insulin_glargine|Glargine]]

[[IntronA_%28Interferon_alpha_2b%29|Intron A]]

[[Lovastatin-Mevacor|Mevacor]]

[[Noxafil|Noxafil]]

[[Ivermectin|Ivermectin]]

[[Vytorin|Vytorin]]

[[Zolinza_%28Vorinostat%29|Zolinza]]

'''2016 Proteopedia Projects'''
----

[[Belsomra|Belsomra]]

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Rebetol|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-12-12T18:12:57Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Students then present their pages to the class as an oral presentation.

'''2016 Proteopedia Projects'''
----

[[Belsomra|Belsomra]]

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Rebetol|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-12-08T19:41:31Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Students then present their pages to the class as an oral presentation.

'''2016 Proteopedia Projects'''
----

[[Belsomra|Belsomra]]

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Ribavirin1|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-12-06T20:01:43Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Below are pages from previous semesters.

'''2016 Proteopedia Projects'''
----

[[Belsomra|Belsomra]]

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Ribavirin1|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-12-06T20:01:12Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Below are pages from previous semesters.

'''2016 Proteopedia Projects'''
----

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Ribavirin1|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-12-06T19:59:56Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Below are pages from previous semesters.

'''2016 Proteopedia Projects'''
----

[[Remicade_%28Infliximab%29|Remicade]]

[[NitroDur|NitroDur]]

[[Januvia_%28sitagliptin%29|Sitagliptin]]

[[Gardasil|Gardasil]]

[[Zepatier|Zepatier]]

[[Fosamax_%28alendronate_sodium%29|Fosamax]]

[[Crixivan|Crixivan]]

[[Invanz_%28Ertapenem%29|Invanz]]

[[Ribavirin1|Ribavirin]]

[[ACE_Inhibitor_Prinivil|Prinivil]]

[[Keytruda|Keytruda]]

[[ACE_Inhibitor_Lisinopril|Lisinopril]]

[[Carbidopa|Carbidopa]]

[[Finasteride|Finasteride]]

[[Victrelis_%28boceprevir%29Victrelis_%28boceprevir%29|Victrelis]]

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

'''2015 Proteopedia Projects'''
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-09-29T19:07:24Z

Christopher Berndsen:

Students in CHEM361 Biochemistry I at James Madison University in groups produce Proteopedia pages based on topics of their choice. Below are pages from previous semesters.

2016 Proteopedia Projects
----

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

2015 Proteopedia Projects
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

Christopher Berndsen/Proteopedia

2016-09-29T18:56:42Z

Christopher Berndsen: New page: == Educational Activities == The Berndsen lab has also taken an active role in using Proteopedia in the Biochemistry classroom and have students use protein structure prediction to underst...

== Educational Activities ==
The Berndsen lab has also taken an active role in using Proteopedia in the Biochemistry classroom and have students use protein structure prediction to understand the molecular basis for disease.

2016 Proteopedia Projects
----

[[Mumps_Virus_Hemagglutinin_Neuraminidase Protein|Mumps Virus]]

[[Human_Erythrocyte_Catalase|Human Erythrocyte Catalase]]

[[TET_Enzymes|TET Enzymes]]

[[XPD_Helicase_%283CRV%29|XPD Helicase]]

[[RING_Finger_Domain_of_BRCA1_and_BARD1_Heterodimer|RING Finger Domain of BRCA1 and BARD1 Heterodimer]]

[[Sucrase-isomaltase|Sucrase isomaltase]]

[[Beta_Secretase_%28BACE1%29_1SGZ|Beta Secretase]]

[[Nos1|Nos1]]

[[Human_gastric_lipase|Human gastric lipase]]

[[Cathepsin_k|Cathepsin k]]

[[STK11|STK11]]

[[TEM1_Class_Antibiotic_Resistance_Proteins|TEM1 Class Antibiotic Resistance Proteins]]

2015 Proteopedia Projects
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

User:Christopher Berndsen/Labinfo

2016-03-01T20:36:20Z

Christopher Berndsen:

==Laboratory Overview==
<Structure load='1WXS' size='350' frame='true' align='right' caption='NMR Structure of the ubiquitin-like protein UFM1' scene='Insert optional scene name here' />
The Berndsen Lab is located in the [http://www.jmu.edu/chemistry/ Department of Chemistry and Biochemistry] at [http://www.jmu.edu James Madison University] in Harrisonburg, VA. The primary research focus is the mechanism enzymes involved in the conjugation and processing of ubiquitin and ubiquitin-like proteins. Additionally, the lab is interested in integrating protein structure research and molecular basis for disease into the biochemistry classroom.

== Research Highlights ==
Ubiquitin and Ubiquitin-like proteins are linked to many cellular functions included protein degradation and DNA damage repair <ref>PMID:15571809</ref><ref>PMID:24699078</ref>. The Berndsen Lab is interested in the catalytic mechanisms the conjugating enzymes E1, E2, and E3 use to attach ubiquitin/ubiquitin-like proteins to the substrate lysine. We are also interested in the proteases that remove these modifications and the chemical mechanism(s) of catalysis. We are currently focused on UFM1 conjugation and the E1 enzyme associated with UFM1, UBA5.

We have also worked on proteins associated with ubiquitin including Ubc13 <ref>PMID:25947351</ref><ref>PMID:23292652</ref>, AMSH <ref>PMID:26601948</ref>, and YUH1.

In addition to our work on enzyme mechanism, we have worked on the structure mechanism of viral tethering by the human protein, BST-2. Recently, we proposed how the disulfides of BST-2 function to increase the strength of BST-2 during viral tethering <ref>PMID:26789136</ref>.

== Educational Activities ==
The Berndsen lab has also taken an active role in using Proteopedia in the Biochemistry classroom and have students use protein structure prediction to understand the molecular basis for disease.

2015 Proteopedia Projects
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''

[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

== References ==
<references/>

User:Christopher Berndsen/Labinfo

2016-03-01T20:35:21Z

Christopher Berndsen:

User:Christopher Berndsen/Labinfo

2016-03-01T20:32:18Z

Christopher Berndsen:

==The Berndsen Laboratory at James Madison University==
<Structure load='1WXS' size='350' frame='true' align='right' caption='NMR Structure of the ubiquitin-like protein UFM1' scene='Insert optional scene name here' />
The Berndsen Lab is located in the [http://www.jmu.edu/chemistry/ Department of Chemistry and Biochemistry] at [http://www.jmu.edu James Madison University] in Harrisonburg, VA. The primary research focus is the mechanism enzymes involved in the conjugation and processing of ubiquitin and ubiquitin-like proteins. Additionally, the lab is interested in integrating protein structure research and molecular basis for disease into the biochemistry classroom.

== Research Highlights ==
Ubiquitin and Ubiquitin-like proteins are linked to many cellular functions included protein degradation and DNA damage repair <ref>PMID:15571809</ref><ref>PMID:24699078</ref>. The Berndsen Lab is interested in the catalytic mechanisms the conjugating enzymes E1, E2, and E3 use to attach ubiquitin/ubiquitin-like proteins to the substrate lysine. We are also interested in the proteases that remove these modifications and the chemical mechanism(s) of catalysis. We are currently focused on UFM1 conjugation and the E1 enzyme associated with UFM1, UBA5.

We have also worked on proteins associated with ubiquitin including Ubc13 <ref>PMID:25947351</ref><ref>PMID:23292652</ref>, AMSH <ref>PMID:26601948</ref>, and YUH1.

In addition to our work on enzyme mechanism, we have worked on the structure mechanism of viral tethering by the human protein, BST-2. Recently, we proposed how the disulfides of BST-2 function to increase the strength of BST-2 during viral tethering <ref>PMID:26789136</ref>.

== Educational Activities ==
The Berndsen lab has also taken an active role in using Proteopedia in the Biochemistry classroom and have students use protein structure prediction to understand the molecular basis for disease.

2015 Proteopedia Projects
----
[[Clathrin_JMU|Clathrin]]

[[5-HT_Receptors|5-HT Receptors]]

[[5-ht3a_receptor|5-HT3a Receptors]]

[[Glut3|Glut3]]

[[Tau|Tau protein]]

[[Dopamine_Receptors|Dopamine receptors]]

[[Cannabinoid_Receptor_1|Cannabinoid Receptor 1]]

[[P.69_Pertactin_Structure_and_Function|Pertactin]]

[[How_Gluten_Protein_Structure_Stimulates_an_Immune_Response|How Gluten Stimulates an Immune Response]]

[[Caffeine]]

[[Calmodulin_JMU|Calmodulin]]

[[Arginine_Kinase_AK|Arginine Kinase]]

[[DeltaFosB|FosB]]

[[GABA_receptor|GABA receptor]]

[[Smallpox_%28Variola_Virus%29_-_Topoisomerase_1B|Smallpox Topoisomerase 1B]]

'''Previous Projects'''
[[Ubc9]]

[[Theoretical_esterases|Theoretical Esterases]]

[[Uba1]]

[[UBC13_MMS2|Ubc13-Mms2]]

[[Ubiquitin_chains|Ubiquitin Chains]]

== References ==
<references/>

User:Christopher Berndsen/Labinfo

2016-03-01T20:09:28Z

Christopher Berndsen:

User:Christopher Berndsen/Labinfo

2016-03-01T20:07:38Z

Christopher Berndsen:

User:Christopher Berndsen/Labinfo

2016-03-01T19:59:57Z

Christopher Berndsen:

User:Christopher Berndsen/Labinfo

2016-03-01T19:42:21Z

Christopher Berndsen:

==The Berndsen Laboratory at James Madison University==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
The Berndsen Lab is located in the [http://www.jmu.edu/chemistry/ Department of Chemistry and Biochemistry] at [http://www.jmu.edu James Madison University] in Harrisonburg, VA. The primary research focus is the mechanism enzymes involved in the conjugation and processing of ubiquitin and ubiquitin-like proteins. Additionally, the lab is interested in integrating protein structure research and molecular basis for disease into the biochemistry classroom.

== Research Highlights ==
Ubiquitin and Ubiquitin-like proteins are linked to many cellular functions included protein degradation and DNA damage repair <ref>PMID:15571809</ref><ref>PMID:24699078</ref>. The Berndsen Lab is interested in the catalytic mechanisms the conjugating enzymes E1, E2, and E3 use to attach ubiquitin/ubiquitin-like proteins to the substrate lysine. We are also interested in the proteases that remove these modifications and the chemical mechanism(s) of catalysis. We are currently focusing on UFM1<Structure load='1WXS' size='350' frame='true' align='right' caption='NMR Structure of UFM1 from <ref>PMID:16527251</ref>' scene='UFM1' />

== Disease ==

== Relevance ==

== Structural highlights ==

</StructureSection>
== References ==
<references/>

User:Christopher Berndsen/Labinfo

2016-03-01T19:39:27Z

Christopher Berndsen:

==The Berndsen Laboratory at James Madison University==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
The Berndsen Lab is located in the [http://www.jmu.edu/chemistry/ Department of Chemistry and Biochemistry] at [http://www.jmu.edu James Madison University] in Harrisonburg, VA. The primary research focus is the mechanism enzymes involved in the conjugation and processing of ubiquitin and ubiquitin-like proteins. Additionally, the lab is interested in integrating protein structure research and molecular basis for disease into the biochemistry classroom.

== Research Highlights ==
Ubiquitin and Ubiquitin-like proteins are linked to many cellular functions included protein degradation and DNA damage repair <ref>PMID:15571809<ref><ref>PMID:24699078<ref>. The Berndsen Lab is interested in the catalytic mechanisms the conjugating enzymes E1, E2, and E3 use to attach ubiquitin/ubiquitin-like proteins to the substrate lysine. We are also interested in the proteases that remove these modifications and the chemical mechanism(s) of catalysis. We are currently focusing on UFM1<Structure load='1WXS' size='350' frame='true' align='right' caption='NMR Structure of UFM1 from <ref>PMID:16527251<ref>' scene='UFM1' />

== Disease ==

== Relevance ==

== Structural highlights ==

</StructureSection>
== References ==
<references/>

User:Christopher Berndsen/Labinfo

2016-03-01T19:05:38Z

Christopher Berndsen:

User:Christopher Berndsen/Labinfo

2016-03-01T18:50:28Z

Christopher Berndsen: New page: ==The Berndsen Laboratory at James Madison University== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> The Berndsen Lab is located in ...

User:Christopher Berndsen

2015-01-07T19:35:01Z

Christopher Berndsen:

*B.S. in Biochemistry, Roanoke College
*Ph.D. in Biomolecular Chemistry, University of Wisconsin-Madison
*Post-doctoral work at Johns Hopkins University in Biophysics and Biophysical Chemistry
*Assistant Professor at James Madison University in the Department of Chemistry and Biochemistry

Ubiquitin chains

2011-08-02T13:39:41Z

Christopher Berndsen: Added jmol scenes of ubiquitin chains.

Ubiquitin chains (or polyubiquitin chains) are protein post-translational modifications that regulate proteasome dependent protein degradation, the cellular response to DNA damage, the inflammatory response and other cellular functions <ref>PMID: 19217402</ref><ref>PMID: 9367341</ref>. Chains begin as a single ubiquitin attached to the modified protein via an isopeptide linkage between a lysine side chain within the substrate protein and the C-terminal glycine of ubiquitin. The chain is built and extended by ubiquitination of ubiquitin on one of the lysines of ubiquitin or the N-terminus. There are a total of seven lysines in ubiquitin (K6, K11, K27, K29, K33, K48, and K63) and chains using all seven lysines have been identified <ref name=Xu>PMID: 19345192</ref>. Chains are frequently referred to in the literature by the lysine position in ubiquitin that connects one ubiquitin to the next. For example, chains built on lysine 48 of ubiquitin are called K48-linked chains. N-terminal to C-terminal connection of ubiquitin molecules is called a linear ubiquitin chain and chains which contain linkages through several lysine positions are called mixed chains <ref>PMID: 18516089</ref>. Ubiquitin chains with different linkages can have different cellular functions some of which are summarized below. The basis for the functional differences between polyubiquitin chains of different linkages were not apparent until the X-ray and NMR structures of several chains were solved.

----

== K48-linked ubiquitin chains ==
<Structure load='2o6v' size='300' frame='true' align='right' caption='K48-linked tetraubiquitin' scene='Ubiquitin_chains/K48_chain_dimer/1' />
K48-linked ubiquitin chains are the primary signal for proteasome dependent degradation of proteins. The attachment of a chain of four or more ubiquitin molecules to a protein is required for efficient degradation. The X-ray crystal structure of K-48 linked diubiquitin<ref name=cook>PMID:1322903</ref> showed inter-ubiquitin interactions between the <scene name='Ubiquitin_chains/K48_chain/2'>hydrophobic patches</scene>(residues L8, I44, V70) of the two molecules. A later X-ray crystal structure of K48-linked tetraubiquitin<ref>PMID: 8107144</ref> showed that the ubiquitin chain adopted a globular tertiary structure which has been described as a <scene name='Ubiquitin_chains/K48_chain_dimer/1'>dimer of ubiquitin dimers </scene>. The interactions between the hydrophobic patches of ubiquitin molecules in 1 and 2 or 3 and 4 were similar to those observed in the diubiquitin structure <ref name=cook/>.
Since the initial structure, several K48-linked tetraubiquitin crystal structures <ref>PMID: 11173499</ref> <ref name=eddins>PMID: 17240395</ref> <ref>PMID: 20823512</ref> have shown there are slight rearrangements of the tertiary structure of the chain dependent upon the pH of the crystallization solution. At pH 6.7, the chain adopts what is known as the closed conformation, because the chain remains in a largely compact form. At pH values less than 4.5, the interaction between diubiquitin molecules becomes weaker and the chain is less compact and there are fewer inter-ubiquitin contacts <ref name=eddins/>. The different tertiary conformations of the polyubiquitin chain are thought to be indicative of the dynamics of the K48-linked ubiquitin chain in the cell. These changes would allow ubiquitin binding proteins to interact with the hydrophobic patches of the ubiquitin molecules<ref>PMID: 9485444</ref>. The structure of cyclic K48-linked tetraubiquitin adopts the same dimer of ubiquitin dimer structure seen in the linear chains <ref>PMID: 20728431</ref>. The authors of this structure suggest this structure demonstrates the inherent flexibility of the ubiquitin chain.

== K63-linked ubiquitin chains ==
<Structure load='3hm3' size='300' frame='true' align='left' caption='Structure of K63-linked tetraubiquitin in hte fully extended conformation. ' scene='Insert optional scene name here' />
K63-linked ubiquitin chains bound to proteins are associated with the DNA damage response and NF-κB signaling <ref>PMID: 21622571</ref>. In contrast to K48-linked tetraubiquitin, the structure of K63-linked ubiquitin is linear, with no inter-ubiquitin contacts apparent in the crystal <ref name=datta>PMID: 19664638</ref><ref>PMID: 19731378</ref>. Small angle X-ray scattering of K63-linked tetraubiquitin confirmed the observations from crystal structures but suggested that a small percentage of chains adopted a partially compacted structure <ref name=datta/>. The specific inter-ubiquitin contacts were not apparent from this experiment. The K63-linked ubiquitin chain binding domains in the signaling proteins NEMO <ref>PMID: 19766637</ref> and Rap80 <ref>PMID: 19536136</ref> bridge the hydrophobic patches of consecutive ubiquitins in the chain through a single alpha helix. The work of Sims and coworkers <ref>PMID: 19328070</ref> showed that decreasing the distance between the ubiquitin interacting motifs in Rap80 decreased the affinity of the Rap80 binding domain for the ubiquitin chain.

== K11-linked ubiquitin chains ==

K11-linked ubiquitin chains are linked to proteasomal degradation and possibly endoplasmic reticulum associated degradation <ref name=Xu/>. The X-ray crystal structure of K11-linked chains shows a compact structure like K48-linked ubiquitin chains <ref name=bremm>PMID: 20622874</ref>. However, the hydrophobic patches which mediate the inter-ubiquitin interactions in K48-linked chains are surface exposed in K11-linked chains. The interaction surface between the two ubiquitins consists of a number of charged and hydrogen bond forming residues. NMR or crystal structures of longer K11-linked chains have not been published to confirm whether this conformation persists with additional ubiquitins.

== Linear ubiquitin chains ==

Linear ubiquitin chains are linked by a peptide bond between the N-terminal alpha-amino group of one ubiquitin and the C-terminus of another ubiquitin. These chains are associated with NF-κB signaling <ref>PMID: 19303852</ref> and some cellular ubiquitin is expressed as linear chains of ubiquitin before processing to monoubiquitin by ubiquitin proteases <ref>PMID: 3041010</ref>. Structurally, linear ubiquitin chains are similar to the extended conformation observed for K63-linked chains <ref>PMID: 19373254</ref>.

== Ubiquitin chains of other linkages ==

As of June 2011, there are not structures available for ubiquitin chains with K6, K27, K29, or K33 linkages. Molecular modeling by Fushman and Walker <ref name=walker>PMID: 19853612</ref> suggest K6 and K27 linked chains will adopt a compact structure similar to that of K48-linked chains, while K29 and K33-linked chains will adopt a more open conformation. The model of K11-linked chains in this study suggests inter-ubiquitin contact between the hydrophobic patches <ref name=walker/>, while the crystal structure suggests these patches are not interacting <ref name=bremm/>. This discrepancy may be because burial of the hydrophobic patch was a restraint in the modeling. Further structural and biochemical work is necessary to determine the correct conformation.

== Chains of Ubiquitin-like proteins (Ubls) ==
<Structure load='1z2m' size='300' frame='true' align='right' caption='Structure of a ISG15 monomer. The tertiary structure consists of two ubiquitin-like folds, resembling a molecule of diubiquitin.' scene='Insert optional scene name here' />
SUMO (Small Ubiquitin-like Modifying Object) does form chains<ref>PMID: 11451954</ref>, however no structural information on these chains is available. Chains of other Ubls may exist, but there is not significant data on their structure and function. The tertiary structure of ISG15 is comprised of two beta grasp folds and is similar in appearance to diubiquitin <ref>PMID: 15917233</ref>. Whether this influences the function of ISG15 is not clear at this time.

==References==

<references />

--[[User:Christopher Berndsen|Christopher Berndsen]] 16:00, 2 August 2011 (IDT)

Ubiquitin chains

2011-08-02T13:00:50Z

Christopher Berndsen: First creation of page

Ubiquitin chains (or polyubiquitin chains) are protein post-translational modifications that regulate proteasome dependent protein degradation, the cellular response to DNA damage, the inflammatory response and other cellular functions <ref>PMID: 19217402</ref><ref>PMID: 9367341</ref>. Chains begin as a single ubiquitin attached to the modified protein via an isopeptide linkage between a lysine side chain within the substrate protein and the C-terminal glycine of ubiquitin. The chain is built and extended by ubiquitination of ubiquitin on one of the lysines of ubiquitin or the N-terminus. There are a total of seven lysines in ubiquitin (K6, K11, K27, K29, K33, K48, and K63) and chains using all seven lysines have been identified <ref name=Xu>PMID: 19345192</ref>. Chains are frequently referred to in the literature by the lysine position in ubiquitin that connects one ubiquitin to the next. For example, chains built on lysine 48 of ubiquitin are called K48-linked chains. N-terminal to C-terminal connection of ubiquitin molecules is called a linear ubiquitin chain and chains which contain linkages through several lysine positions are called mixed chains <ref>PMID: 18516089</ref>. Ubiquitin chains with different linkages can have different cellular functions some of which are summarized below. The basis for the functional differences between polyubiquitin chains of different linkages were not apparent until the X-ray and NMR structures of several chains were solved.

----

== K48-linked ubiquitin chains ==

K48-linked ubiquitin chains are the primary signal for proteasome dependent degradation of proteins. The attachment of a chain of four or more ubiquitin molecules to a protein is required for efficient degradation. The X-ray crystal structure of K-48 linked diubiquitin<ref name=cook>PMID:1322903</ref> showed inter-ubiquitin interactions between the hydrophobic patches (residues L8, I44, V70) of the two molecules. A later X-ray crystal structure of K48-linked tetraubiquitin<ref>PMID: 8107144</ref> showed that the ubiquitin chain adopted a globular tertiary structure which has been described as a “dimer of ubiquitin dimers”. The interactions between the hydrophobic patches of ubiquitin molecules in 1 and 2 or 3 and 4 were similar to those observed in the diubiquitin structure <ref name=cook/>.
Since the initial structure, several K48-linked tetraubiquitin crystal structures <ref>PMID: 11173499</ref> <ref name=eddins>PMID: 17240395</ref> <ref>PMID: 20823512</ref> have shown there are slight rearrangements of the tertiary structure of the chain dependent upon the pH of the crystallization solution. At pH 6.7, the chain adopts what is known as the closed conformation, because the chain remains in a largely compact form. At pH values less than 4.5, the interaction between diubiquitin molecules becomes weaker and the chain is less compact and there are fewer inter-ubiquitin contacts <ref name=eddins/>. The different tertiary conformations of the polyubiquitin chain are thought to be indicative of the dynamics of the K48-linked ubiquitin chain in the cell. These changes would allow ubiquitin binding proteins to interact with the hydrophobic patches of the ubiquitin molecules<ref>PMID: 9485444</ref>. The structure of cyclic K48-linked tetraubiquitin adopts the same dimer of ubiquitin dimer structure seen in the linear chains <ref>PMID: 20728431</ref>. The authors of this structure suggest this structure demonstrates the inherent flexibility of the ubiquitin chain.

== K63-linked ubiquitin chains ==

K63-linked ubiquitin chains bound to proteins are associated with the DNA damage response and NF-κB signaling <ref>PMID: 21622571</ref>. In contrast to K48-linked tetraubiquitin, the structure of K63-linked ubiquitin is linear, with no inter-ubiquitin contacts apparent in the crystal <ref name=datta>PMID: 19664638</ref><ref>PMID: 19731378</ref>. Small angle X-ray scattering of K63-linked tetraubiquitin confirmed the observations from crystal structures but suggested that a small percentage of chains adopted a partially compacted structure <ref name=datta/>. The specific inter-ubiquitin contacts were not apparent from this experiment. The K63-linked ubiquitin chain binding domains in the signaling proteins NEMO <ref>PMID: 19766637</ref> and Rap80 <ref>PMID: 19536136</ref> bridge the hydrophobic patches of consecutive ubiquitins in the chain through a single alpha helix. The work of Sims and coworkers <ref>PMID: 19328070</ref> showed that decreasing the distance between the ubiquitin interacting motifs in Rap80 decreased the affinity of the Rap80 binding domain for the ubiquitin chain.

== K11-linked ubiquitin chains ==

K11-linked ubiquitin chains are linked to proteasomal degradation and possibly endoplasmic reticulum associated degradation <ref name=Xu/>. The X-ray crystal structure of K11-linked chains shows a compact structure like K48-linked ubiquitin chains <ref name=bremm>PMID: 20622874</ref>. However, the hydrophobic patches which mediate the inter-ubiquitin interactions in K48-linked chains are surface exposed in K11-linked chains. The interaction surface between the two ubiquitins consists of a number of charged and hydrogen bond forming residues. NMR or crystal structures of longer K11-linked chains have not been published to confirm whether this conformation persists with additional ubiquitins.

== Linear ubiquitin chains ==

Linear ubiquitin chains are linked by a peptide bond between the N-terminal alpha-amino group of one ubiquitin and the C-terminus of another ubiquitin. These chains are associated with NF-κB signaling <ref>PMID: 19303852</ref> and some cellular ubiquitin is expressed as linear chains of ubiquitin before processing to monoubiquitin by ubiquitin proteases <ref>PMID: 3041010</ref>. Structurally, linear ubiquitin chains are similar to the extended conformation observed for K63-linked chains <ref>PMID: 19373254</ref>.

== Ubiquitin chains of other linkages ==

As of June 2011, there are not structures available for ubiquitin chains with K6, K27, K29, or K33 linkages. Molecular modeling by Fushman and Walker <ref name=walker>PMID: 19853612</ref> suggest K6 and K27 linked chains will adopt a compact structure similar to that of K48-linked chains, while K29 and K33-linked chains will adopt a more open conformation. The model of K11-linked chains in this study suggests inter-ubiquitin contact between the hydrophobic patches <ref name=walker/>, while the crystal structure suggests these patches are not interacting <ref name=bremm/>. This discrepancy may be because burial of the hydrophobic patch was a restraint in the modeling. Further structural and biochemical work is necessary to determine the correct conformation.

== Chains of Ubiquitin-like proteins (Ubls) ==

SUMO (Small Ubiquitin-like Modifying Object) does form chains<ref>PMID: 11451954</ref>, however no structural information on these chains is available. Chains of other Ubls may exist, but there is not significant data on their structure and function. The tertiary structure of ISG15 is comprised of two beta grasp folds and is similar in appearance to diubiquitin <ref>PMID: 15917233</ref>. Whether this influences the function of ISG15 is not clear at this time.

==References==

<references />

--[[User:Christopher Berndsen|Christopher Berndsen]] 16:00, 2 August 2011 (IDT)