Presentation is loading. Please wait.

Presentation is loading. Please wait.

Amino Acid Sequences in V3 Loop Conformation

Published bySuharto Sudjarwadi Modified over 5 years ago

Similar presentations

Presentation on theme: "Amino Acid Sequences in V3 Loop Conformation"— Presentation transcript:

1 Amino Acid Sequences in V3 Loop Conformation
Alex Cardenas, Bobby Arnold and Zeb Russo Loyola Marymount University Department of Biology BIO /02/11

2 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

3 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

4 CD4 T cell count is an trait in developing AIDs ( >200 safe, <200 AIDs)
Observations led us to conclude that CD4 T cell counts were crucial in developing AIDs. Rapid Progressors – 1, 3, 4, 10, 11, 15. Controls Moderate progressor – 6. Non Progessor – 13.

5 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

6 CD4 T cell count and relationship to V3 loop amino acid sequence
We were interested in the amino acid sequences of AIDs subjects. Our question Is there a conserved region in the V3 loop sequence that led the subject to develop AIDs?

7 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

8 Usage of Star Biochem and to Answer our Question
Star Biochem was used to determine the location and structure of the V3 loop region ProtParam was considered as a tool to use, however all the variable regions were determined to be coils so therefore was not necessary

9 gp120 Secondary Structure Using Star Biochem Kwong et. al
V3 region

10 V3 region Secondary Structure Stanfield et. al
1NAK

11 Stanfield et. al 2ndary Structure not useful in our examination of Markham data
Stanfield data composed of amino acid chains Markham data composed of amino acid chains

12 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

13 BioWorkbench used to create multiple sequence alignments
Each rapid progressor subject had a clone randomly chosen from their first and last visit Control subjects had one clone randomly selected from last visit. Each rapid progressor had their two sequences aligned Control subjects were aligned with each other All rapid progressor last visits were aligned with and without a control sequence

14 ClustalW Multiple Sequence Alignment Results
Single Subject Alignments Multiple Subject Alignments

15 Outline CD4 T cell count is a trait in developing AIDs ( >200 safe, <200 AIDs). Differing CD4 T cell count is correlated with conservation in amino acid sequences. Usage of Star Biochem to Answer our Question BioWorkbench used to create multiple sequence alignments Results obtained from multiple sequence were observed and analyzed. Discussion and thoughts of our findings are shared.

16

17

18

Download ppt "Amino Acid Sequences in V3 Loop Conformation"

Similar presentations

Changes In Protein Sequences Of the HIV-1 gp120 V3 Region In Non-Progressor Types Nicki S.Harmon Samantha M. Hurndon.

Changes In Protein Sequences Of the HIV-1 gp120 V3 Region In Non-Progressor Types Nicki S.Harmon Samantha M. Hurndon.
Genetic Similarities Between HIV-1 Viruses in the Onset of AIDS Isabel Gonzaga BIOL 368-01: Bioinformatics Laboratory Loyola Marymount University October.

Genetic Similarities Between HIV-1 Viruses in the Onset of AIDS Isabel Gonzaga BIOL : Bioinformatics Laboratory Loyola Marymount University October.
Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs RL Stanfield, E Cabezas, AC Satterthwait, EA Stura, AT Profy,

Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs RL Stanfield, E Cabezas, AC Satterthwait, EA Stura, AT Profy,
An Introduction to the HIV Problem Space Oakwood University: Faculty Quantitative Institute Aug. 10–12, 2009.

An Introduction to the HIV Problem Space Oakwood University: Faculty Quantitative Institute Aug. 10–12, 2009.
Examination of Amino Acid Differences as a Means of Determining Functional Changes in HIV-1 Protein Sequences Chris Rhodes and Isaiah Castaneda Loyola.

Examination of Amino Acid Differences as a Means of Determining Functional Changes in HIV-1 Protein Sequences Chris Rhodes and Isaiah Castaneda Loyola.
Analysis of HIV Evolution Bobak Seddighzadeh and Kristoffer Chin Department of Biology Loyola Marymount University Bio 398-01 February 23, 2010.

Analysis of HIV Evolution Bobak Seddighzadeh and Kristoffer Chin Department of Biology Loyola Marymount University Bio February 23, 2010.
Multiple Sequence Alignment May 12, 2009 Announcements Quiz #2 return (average 30) Hand in homework #7 Learning objectives-Understand ClustalW Homework#8-Due.

Multiple Sequence Alignment May 12, 2009 Announcements Quiz #2 return (average 30) Hand in homework #7 Learning objectives-Understand ClustalW Homework#8-Due.
Examining Subjects of HIV-1 With Possible Predominant Viral Strains Samantha Hurndon Isaiah Castaneda.

Examining Subjects of HIV-1 With Possible Predominant Viral Strains Samantha Hurndon Isaiah Castaneda.
Unconserved Amino Acid Sequences in V3 Domain of gp120 Show No Significant Correlation to Altered Folding and Function Bobak Seddighzadeh Alex George.

Unconserved Amino Acid Sequences in V3 Domain of gp120 Show No Significant Correlation to Altered Folding and Function Bobak Seddighzadeh Alex George.
STEPHANIE HINTZEN BIOL 471 SIV and HIV: Differences in Diversity and Divergence.

STEPHANIE HINTZEN BIOL 471 SIV and HIV: Differences in Diversity and Divergence.
Re evaluating the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates Angela Garibaldi & Ryan Willhite Loyola Marymount University.

Re evaluating the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates Angela Garibaldi & Ryan Willhite Loyola Marymount University.
A Mutational Investigation of an HIV Patient’s GP120 Glycoprotein and it’s Implications on CD4 Binding Salita Kaistha Usrinus College, Collegeville PA.

A Mutational Investigation of an HIV Patient’s GP120 Glycoprotein and it’s Implications on CD4 Binding Salita Kaistha Usrinus College, Collegeville PA.
Predicting the Onset of AIDS Robert Arnold, Alex Cardenas, Zeb Russo LMU Biology Department 10/5/2011.

Predicting the Onset of AIDS Robert Arnold, Alex Cardenas, Zeb Russo LMU Biology Department 10/5/2011.
Supporting Scientific Collaboration Online SCOPE Workshop at San Diego Supercomputer Center March 19-22, 2008.

Supporting Scientific Collaboration Online SCOPE Workshop at San Diego Supercomputer Center March 19-22, 2008.
Patterns of selection for or against amino acid change among different CD4 T-cell count progressor groups Michael Pina, Salomon Garcia Journal Club Presentation.

Patterns of selection for or against amino acid change among different CD4 T-cell count progressor groups Michael Pina, Salomon Garcia Journal Club Presentation.
Diversity and Divergence in HIV-1 Viral Variants between patients with high CD4+ T Cell Variability and Patients with Rapid CD4+ T Cell Decline Kevin Paiz-Ramirez.

Diversity and Divergence in HIV-1 Viral Variants between patients with high CD4+ T Cell Variability and Patients with Rapid CD4+ T Cell Decline Kevin Paiz-Ramirez.
Mutations on the V3 loop of gp120 may predict progression to AIDS Derese Getnet, Dr. Rebecca Roberts, Structural Biology, Ursinus College, Collegeville.

Mutations on the V3 loop of gp120 may predict progression to AIDS Derese Getnet, Dr. Rebecca Roberts, Structural Biology, Ursinus College, Collegeville.
Amino Acid Sequences in V3 Loop Conformation Alex Cardenas, Bobby Arnold and Zeb Russo Loyola Marymount University Department of Biology BIO 398 11/02/11.

Amino Acid Sequences in V3 Loop Conformation Alex Cardenas, Bobby Arnold and Zeb Russo Loyola Marymount University Department of Biology BIO /02/11.
Predicting the Onset of AIDS Robert Arnold, Alex Cardenas, Zeb Russo LMU Biology Department 10/5/2011.

Predicting the Onset of AIDS Robert Arnold, Alex Cardenas, Zeb Russo LMU Biology Department 10/5/2011.
Residue Sequence and Structure in the Re evaluation the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates Angela Garibaldi.

Residue Sequence and Structure in the Re evaluation the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates Angela Garibaldi.

Similar presentations

Ads by Google