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

Slides:

Advertisements

Similar presentations

Genetic Similarities Between HIV-1 Viruses in the Onset of AIDS Isabel Gonzaga BIOL : Bioinformatics Laboratory Loyola Marymount University October.

Advertisements

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,

Mutations Section 12–4 This section describes and compares gene mutations and chromosomal mutations.

HIV GP120 Envelope Protein

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.

Analysis of HIV Evolution Bobak Seddighzadeh and Kristoffer Chin Department of Biology Loyola Marymount University Bio February 23, 2010.

Antibodies I’ve heard of them but just what are they? Plasma Cells of Effector Cells Transcription Translation Polypeptide / Proteins Humoral Response:

Examining Subjects of HIV-1 With Possible Predominant Viral Strains Samantha Hurndon Isaiah Castaneda.

How do proteins fold? Folding in a test-tube The structure of proteins is determined by the amino acid sequence; many proteins in solution can be unfolded.

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

Unconserved Amino Acid Sequences in V3 Domain of gp120 Show No Significant Correlation to Altered Folding and Function Bobak Seddighzadeh Alex George.

Comparison of p53 Structure: Wild type vs. mutant What change in wild type p53 may lead to cancer?

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.

Construction of Substitution Matrices

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.

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.

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.

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

Project in BioInformatics Variability of Membrane proteins of different HIV strains By Emad Nimer Wisam Kadry.

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.

Examining Subjects of HIV-1 With Possible Predominant Viral Strains Samantha Hurndon Isaiah Castaneda.

Role of V3 in HIV Entry and Neutralization Chloe Jones, Isabel Gonzaga, and Nicole Anguiano BIOL398: Bioinformatics Laboratory Loyola Marymount University.

Analyzing Differences in Protein Sequences Between Subjects with Varying T Cell Counts J’aime Moehlman Amanda Wavrin Loyola Marymount University March.

3DM: Protein Super-family Platforms 3DM Protein super-family data integration Tom van den Bergh Bio-Prodict.

Changes In Protein Sequences Of the HIV-1 gp120 V3 Region In Non-Progressor Types Nicki S.Harmon Samantha M. Hurndon LMU Department of Biology BIOL 368.

Construction of Substitution matrices

Examining the Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Examining Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano Bioinformatics Laboratory Loyola.

V3 Loop Binding to CCR5 and CXCR4 of Rapid and Non Progressor HIV Patients in Baltimore MD BackgroundCCR5 and CXCR4 Receptor Rapid-progressor Patient 10.

Structure of V3-containing HIV-1 gp120 core Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., Dimitrov, D. S., Korber,

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

Examining Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Investigations of HIV-1 Env Evolution Evolutionary Bioinformatics Education: A BioQUEST Curriculum Consortium Approach Grand Valley State University August.

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A,

HIV ‐ 1 replication activates CD4 + T cells with specificities for persistent herpes viruses by Anna Haas, Manuela Rehr, Frederik Graw, Peter Rusert, Walter.

MdSFBB3-alpha MSHVRESETPEDRVVEILSRLPPKSLMRFKCIHKSWFSLINNLSFVAKHLSNSVDNKLSSSTCILLNRSQAHIFPDQSWKQEVFWSMINFSIDSDENNLHYDVEDLN-IP 109 MdSFBB3-beta MSQVHESETPEDKVVEILCRLPPKSLMRFKCIRKSWCTLINRPSFVAKHLNNSVDNKLSSSTCILLNRSQAHIFPDQSWKQEVFWSTINLSIDSDEHNLHYDVEDLI-IP.

Journal Club Presentation BIOL368/F16: Bioinformatics Laboratory

Amino Acid Sequences in V3 Loop Conformation

The V3 Region Expresses More Diversity in Amino Acid Sequence in AIDS Diagnosed Patients than in Non-Trending and AIDS Progressing Patients HIV Structure.

Do HIV+ Rapid Progressors Show More Divergence than Non-Progressors?

Amino Acid Sequences in V3 Loop Conformation

Peter D. Kwong, John R. Mascola Immunity

There are four levels of structure in proteins

Predicting the Onset of AIDS

Volume 9, Issue 2, Pages (February 2002)

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A,

Investigations of HIV-1 Env Evolution

Loyola Marymount University

LMU Department of Biology

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,

Predicting the Onset of AIDS

Loyola Marymount University

Loyola Marymount University

Nicki Harmon, Samantha Hurndon, & Zeb Russo

Amino Acid Sequences in V3 Loop Conformation

Crystal Structure of the Human High-Affinity IgE Receptor

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A,

Volume 3, Issue 1, Pages (January 2013)

Predicting the Onset of AIDS

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

Chloe Jones, Isabel Gonzaga, and Nicole Anguiano

Loyola Marymount University

Guilty as charged Cancer Cell

Presentation transcript:

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

Outline Markham’s non-progressors

The Amino Acid Sequence of the V3 Region Plays A Significant Role in CD4 Binding. The V3 region of the gp 120 env protein is a variable loop with a high mutation rate. V3 is what binds to the CD4 receptor sites on cell. The amino acid sequence determines how the V3 region will function. – And therefore, how the CD4 will interact

HIV-1 Progresses at Different Rate Markham observed 3 types of progressors – Non-progressors Maintained CD4 T cell levels above 650 throughout the Observation period. – Moderate CD4 T cell levels declined to during the observation period – Rapid Having attained a level of fewer than 200 CD4 T cells

The Non-Progressor Types Should Have Amino Acid Sequences that are Closely Related

Methods were Based off Markham’s Findings The subjects that we selected for our study were subjects 2, 12, 13 and 8. Subject 2, 12 and 13 are non progressor types Subject 8 is a moderate progressor that will be used as a comparison to our non progressor subjects

Determination of Sequence were Randomly Selected Due to the nature of the non-progressor type, sequence selection can be random. Subject 8 showed a change over the course of the study. Due to this change sequences from the first and last visits were chosen.

Amino Acid Sequences were Retrieved For Our Subjects The program Bedrock was use to access our sequences.

Analysis of Multiple Sequences Alignment Shows Conservation of Residues

Secondary Structure Is Maintained Throughout The Subjects

Based Off Sequences From Subjects 2, 12, 13 & 8 We Can Conclude that The Non-Progressor types had similar amino acid sequences. There were changes between the non- progressors and subject 8 that could account for subject 8 being a moderate progressor. Secondary structure was not affected by these changes in sequence.

References Positive In Vivo Selection of the HIV-1 Envelope Protein gp120 Occurs at Surface-Exposed Regions Beda Joos1, Beda Joos1 Marek Fischer1, Marek Fischer1 Andreas Schweizer1, Andreas Schweizer1 Herbert Kuster1, Herbert Kuster1 Jürg Böni2, Jürg Böni2 Joseph K. Wong3, Joseph K. Wong3 Rainer Weber1, Rainer Weber1 Alexandra Trkola1 and Alexandra Trkola1 Huldrych F. Günthard1 Huldrych F. Günthard1