scholarly journals Teaching Structure with Molecular Visualization Tools. A Crash Course from Small Molecules to the HIV-1 Protease for Undergraduate Students

2021 ◽  
Vol 5 (2) ◽  
pp. 209
Author(s):  
Paraskevi E Mpeza
Keyword(s):  
Biological Sciences ◽  
Undergraduate Students ◽  
Protein Molecule ◽  
Molecular Visualization ◽  
Inquiry Based Learning ◽  
Immunodeficiency Virus ◽  
Visualization Tools ◽  
Simple Molecules ◽  
And Function ◽  
Hiv 1

One of the challenges in the teaching of chemistry to students in higher education is their introduction to the visualization and molecular depiction software, deepening thus their understanding and creating new conceptions in the physical and biological sciences. This paper describes the implementation of a learning unit for 1st and 2nd semester undergraduate students (that were not previously exposed to molecular visualizations) in agricultural technology for chemistry and biochemistry courses respectively. A series of educational activities are presented beginning with the use of simple molecular models as plastic and wooden balls for atoms and sticks for bonds, to enhance the previous knowledge of the 2-D structural conformations. The students are introduced in depth to the theory of chemical bonding, molecular shapes, and polarity. This represents a continuum of increased complexity in inquiry-based learning, starting from simple molecules and ending with the exploration of the shape and function of a protein molecule, such as the human immunodeficiency virus (HIV)-1 protease; Thus easily leads to the study of the interactions between this protease and inhibitory drugs, via freely-available software tools. The gains in the students’ understanding and help for future courses and their career are analyzed.

scholarly journals Structure and Function of CC-Chemokine Receptor 5 Homologues Derived from Representative Primate Species and Subspecies of the Taxonomic Suborders Prosimii and Anthropoidea

2003 ◽  
Vol 77 (22) ◽  
pp. 12310-12318 ◽  
Author(s):  
Kevin J. Kunstman ◽  
Bridget Puffer ◽  
Bette T. Korber ◽  
Carla Kuiken ◽  
Una R. Smith ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chemokine Receptor ◽  
Transmembrane Domain ◽  
Structure And Function ◽  
Primate Species ◽  
Amino Acid Substitutions ◽  
Immunodeficiency Virus ◽  
And Function ◽  
Cc Chemokine Receptor 5 ◽  
Hiv 1

ABSTRACT A chemokine receptor from the seven-transmembrane-domain G-protein-coupled receptor superfamily is an essential coreceptor for the cellular entry of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) strains. To investigate nonhuman primate CC-chemokine receptor 5 (CCR5) homologue structure and function, we amplified CCR5 DNA sequences from peripheral blood cells obtained from 24 representative species and subspecies of the primate suborders Prosimii (family Lemuridae) and Anthropoidea (families Cebidae, Callitrichidae, Cercopithecidae, Hylobatidae, and Pongidae) by PCR with primers flanking the coding region of the gene. Full-length CCR5 was inserted into pCDNA3.1, and multiple clones were sequenced to permit discrimination of both alleles. Compared to the human CCR5 sequence, the CCR5 sequences of the Lemuridae, Cebidae, and Cercopithecidae shared 87, 91 to 92, and 96 to 99% amino acid sequence homology, respectively. Amino acid substitutions tended to cluster in the amino and carboxy termini, the first transmembrane domain, and the second extracellular loop, with a pattern of species-specific changes that characterized CCR5 homologues from primates within a given family. At variance with humans, all primate species examined from the suborder Anthropoidea had amino acid substitutions at positions 13 (N to D) and 129 (V to I); the former change is critical for CD4-independent binding of SIV to CCR5. Within the Cebidae, Cercopithecidae, and Pongidae (including humans), CCR5 nucleotide similarities were 95.2 to 97.4, 98.0 to 99.5, and 98.3 to 99.3%, respectively. Despite this low genetic diversity, the phylogeny of the selected primate CCR5 homologue sequences agrees with present primate systematics, apart from some intermingling of species of the Cebidae and Cercopithecidae. Constructed HOS.CD4 cell lines expressing the entire CCR5 homologue protein from each of the Anthropoidea species and subspecies were tested for their ability to support HIV-1 and SIV entry and membrane fusion. Other than that of Cercopithecus pygerythrus, all CCR5 homologues tested were able to support both SIV and HIV-1 entry. Our results suggest that the shared structure and function of primate CCR5 homologue proteins would not impede the movement of primate immunodeficiency viruses between species.

scholarly journals Effects of the SOS (A501C/T605C) and DS (I201C/A433C) Disulfide Bonds on HIV-1 Membrane Envelope Glycoprotein Conformation and Function

2019 ◽  
Vol 93 (12) ◽  
Author(s):  
Hanh T. Nguyen ◽  
Nirmin Alsahafi ◽  
Andrés Finzi ◽  
Joseph G. Sodroski
Keyword(s):  
Envelope Glycoprotein ◽  
Disulfide Bonds ◽  
Virus Entry ◽  
Envelope Proteins ◽  
Immunodeficiency Virus ◽  
Membrane Envelope ◽  
And Function ◽  
State 1 ◽  
Hiv 1

ABSTRACTMost broadly neutralizing antibodies and many entry inhibitors target the pretriggered (state 1) conformation of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env). Here we examine two previously reported Env mutants designed to be stabilized in this conformation by the introduction of artificial disulfide bonds: A501C/T605C (called SOS) and I201C/A433C (called DS). SOS Env supported virus entry and cell-cell fusion only after exposure to a reducing agent, dithiothreitol (DTT). Deletion of the Env cytoplasmic tail improved the efficiency with which the SOS Env supported virus infection in a reducing environment. The antigenicity of the SOS Env was similar to that of the unmodified Env, except for greater sensitivity to some state 1-preferring ligands. In contrast, viruses with the DS Env were not infectious, even after DTT treatment. The proteolytic maturation of the DS Env on both cell surfaces and virions was severely compromised compared with that of the unmodified Env. The DS Env exhibited detectable cell-fusing activity when DTT was present. However, the profiles of cell-surface Env recognition and cell-cell fusion inhibition by antibodies differed for the DS Env and the unmodified Env. Thus, the DS Env appears to be stabilized in an off-pathway conformation that is nonfunctional on the virus. The SOS change exerted more subtle, context-dependent effects on Env conformation and function.IMPORTANCEThe human immunodeficiency virus type 1 (HIV-1) envelope proteins (Envs) bind receptors on the host cell and change shape to allow the virus to enter the cell. Most virus-inhibiting antibodies and drugs recognize a particular shape of Env called state 1. Disulfide bonds formed by cysteine residues have been introduced into soluble forms of the flexible envelope proteins in an attempt to lock them into state 1 for use in vaccines and as research tools. We evaluated the effect of these cysteine substitutions on the ability of the membrane Env to support virus entry and on susceptibility to inhibition by antibodies and small molecules. We found that the conformation of the envelope proteins with the cysteine substitutions differed from that of the unmodified membrane envelope proteins. Awareness of these effects can assist efforts to create stable HIV-1 Env complexes that more closely resemble the state 1 conformation.

scholarly journals Ineffectual Targeting of HIV-1 Nef by Cytotoxic T Lymphocytes in Acute Infection Results in No Functional Impairment or Viremia Reduction

2014 ◽  
Vol 88 (14) ◽  
pp. 7881-7892 ◽  
Author(s):  
Justin De La Cruz ◽  
Thomas Vollbrecht ◽  
Patricia Frohnen ◽  
Hwee L. Ng ◽  
Eric S. Daar ◽  
...  
Keyword(s):  
T Lymphocytes ◽  
Receptor Gene ◽  
Acute Infection ◽  
Cell Receptor ◽  
Immunodeficiency Virus ◽  
Successful Control ◽  
And Function ◽  
Hiv 1 ◽  
Ctl Responses

ABSTRACTThe human immunodeficiency virus type 1 (HIV-1) accessory protein Nef is heavily targeted by CD8+T lymphocytes (CTLs) during acute infection and therefore is included in many candidate vaccines. We investigated whether CTL targeting of Nef during acute infection contributes to immune control by disrupting the function of Nef. The sequence and function of Nef in parallel with CTL responses were assessed longitudinally from peak viremia until the viremia set point in a cohort of six subjects with acute infection. All but one individual had a single founder strain. Nef-specific CTL responses were detected in all subjects and declined in magnitude over time. These responses were associated with mutations, but none of the mutations were detected in important functional motifs. Nef-mediated downregulation of CD4 and major histocompatibility complex (MHC) class I molecules was better preserved in acute infection than in chronic infection. Finally, Nef-specific CTL responses were not associated with a reduction in viremia from its acute-phase peak. Our results indicate that CTLs targeting Nef epitopes outside critical functional domains have little effect on the pathogenic functions of Nef, rendering these responses ineffective in acute infection.IMPORTANCEThese data indicate that using the whole Nef protein as a vaccine immunogen likely allows immunodominance that leads to targeting of CTL responses that are rapidly escaped with little effect on Nef-mediated pathogenic functions. Pursuing vaccination approaches that can more precisely direct responses to vulnerable areas would maximize efficacy. Until vaccine-induced targeting can be optimized, other approaches, such as the use of Nef function inhibitors or the pursuit of immunotherapies such as T cell receptor gene therapy or adoptive transfer, may be more likely to result in successful control of viremia.

scholarly journals Evolution in the Courtroom: Using Phylogenetics to Investigate Legal Claims of HIV Transmission

2020 ◽  
Author(s):  
Benjamin Toups ◽  
Jeremy M. Brown
Keyword(s):  
Biological Sciences ◽  
Dna Sequences ◽  
Hiv Transmission ◽  
Rapid Evolution ◽  
Rapid Rate ◽  
The Public ◽  
Rates Of Evolution ◽  
Immunodeficiency Virus ◽  
Hiv 1 ◽  
Fast Rates

DNA sequences have become ubiquitous across the biological sciences and are even embedded in the public psyche, perhaps most famously in the context of forensic science. A human being’s DNA changes very little over his or her lifetime, and this inherent stability lends itself well to positively identifying individuals using DNA samples. However, not all genomes are so stable, even over short timespans. One particularly dramatic example is human immunodeficiency virus (HIV-1). Unlike the human genome, the HIV-1 genome has an extraordinarily high mutation rate. This, in combination with recombination, rapid proliferation, and strong selection exerted by host immune systems, leads to exceptionally fast rates of evolution. The result of these interacting processes is a population of diverse and dynamically evolving HIV-1 genomes in the host, which is one reason why the virus is so difficult to eradicate. HIV-1’s rapid rate of evolution also prevents the use of standard DNA fingerprinting techniques that rely on stable, unchanging genomes to connect the infections in different individuals, but such rapid evolution does lend itself particularly well to phylogenetic analysis.

A Synthetic Peptide Derived From Human Immunodeficiency Virus Type 1 gp120 Downregulates the Expression and Function of Chemokine Receptors CCR5 and CXCR4 in Monocytes by Activating the 7-Transmembrane G-Protein–Coupled Receptor FPRL1/LXA4R

Blood ◽  
1999 ◽  
Vol 94 (4) ◽  
pp. 1165-1173
Author(s):  
Xiyun Deng ◽  
Hirotsugu Ueda ◽  
Shao Bo Su ◽  
Wanghua Gong ◽  
Nancy M. Dunlop ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
G Protein ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Synthetic Peptide ◽  
Immunodeficiency Virus ◽  
And Function ◽  
G Protein Coupled ◽  
Hiv 1

Because envelope gp120 of various strains of human immunodeficiency virus type 1 (HIV-1) downregulates the expression and function of a variety of chemoattractant receptors through a process of heterologous desensitization, we investigated whether epitopes derived from gp120 could mimic the effect. A synthetic peptide domain, designated F peptide, corresponding to amino acid residues 414-434 in the V4-C4 region of gp120 of the HIV-1 Bru strain, potently reduced monocyte binding and chemotaxis response to macrophage inflammatory protein 1β (MIP-1β) and stromal cell-derived factor 1 (SDF-1), chemokines that use the receptors CCR5 and CXCR4, respectively. Further study showed that F peptide by itself is an inducer of chemotaxis and calcium mobilization in human monocytes and neutrophils. In cross-desensitization experiments, among the numerous chemoattractants tested, only the bacterial chemotactic peptide fMLF, when used at high concentrations, partially attenuated calcium mobilization induced by F peptide in phagocytes, suggesting that this peptide domain might share a 7-transmembrane, G-protein–coupled receptor with fMLF. By using cells transfected with cDNAs encoding receptors that interact with fMLF, we found that F peptide uses an fMLF receptor variant, FPRL1, as a functional receptor. The activation of monocytes by F peptide resulted in downregulation of the cell surface expression of CCR5 and CXCR4 in a protein kinase C-dependent manner. These results demonstrate that activation of FPRL1 on human moncytes by a peptide domain derived from HIV-1 gp120 could lead to desensitization of cell response to other chemoattractants. This may explain, at least in part, the initial activation of innate immune responses in HIV-1–infected patients followed by immune suppression.

scholarly journals Evolution-Guided Structural and Functional Analyses of the HERC Family Reveal an Ancient Marine Origin and Determinants of Antiviral Activity

2018 ◽  
Vol 92 (13) ◽  
pp. e00528-18 ◽  
Author(s):  
Ermela Paparisto ◽  
Matthew W. Woods ◽  
Macon D. Coleman ◽  
Seyed A. Moghadasi ◽  
Divjyot S. Kochar ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Particle Production ◽  
Structural Topology ◽  
Antiviral Protein ◽  
Intrinsic Immunity ◽  
Marine Origin ◽  
Immunodeficiency Virus ◽  
And Function ◽  
Functional Analyses ◽  
Hiv 1

ABSTRACTIn humans, homologous to the E6-AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing protein 5 (HERC5) is an interferon-induced protein that inhibits replication of evolutionarily diverse viruses, including human immunodeficiency virus type 1 (HIV-1). To better understand the origin, evolution, and function of HERC5, we performed phylogenetic, structural, and functional analyses of the entire human small-HERC family, which includes HERC3, HERC4, HERC5, and HERC6. We demonstrated that theHERCfamily emerged >595 million years ago and has undergone gene duplication and gene loss events throughout its evolution. The structural topology of the RCC1-like domain and HECT domains from all HERC paralogs is highly conserved among evolutionarily diverse vertebrates despite low sequence homology. Functional analyses showed that the human small HERCs exhibit different degrees of antiviral activity toward HIV-1 and that HERC5 provides the strongest inhibition. Notably, coelacanth HERC5 inhibited simian immunodeficiency virus (SIV), but not HIV-1, particle production, suggesting that the antiviral activity of HERC5 emerged over 413 million years ago and exhibits species- and virus-specific restriction. In addition, we showed that both HERC5 and HERC6 are evolving under strong positive selection, particularly blade 1 of the RCC1-like domain, which we showed is a key determinant of antiviral activity. These studies provide insight into the origin, evolution, and biological importance of the human restriction factor HERC5 and the other HERC family members.IMPORTANCEIntrinsic immunity plays an important role as the first line of defense against viruses. Studying the origins, evolution, and functions of proteins responsible for effecting this defense will provide key information about virus-host relationships that can be exploited for future drug development. We showed that HERC5 is one such antiviral protein that belongs to an evolutionarily conserved family of HERCs with an ancient marine origin. Not all vertebrates possess all HERC members, suggesting that different HERCs emerged at different times during evolution to provide the host with a survival advantage. Consistent with this, two of the more recently emerged HERC members, HERC5 and HERC6, displayed strong signatures of having been involved in an ancient evolutionary battle with viruses. Our findings provide new insights into the evolutionary origin and function of the HERC family in vertebrate evolution, identifying HERC5 and possibly HERC6 as important effectors of intrinsic immunity in vertebrates.

scholarly journals Anti-CXCR4 Monoclonal Antibodies Recognizing Overlapping Epitopes Differ Significantly in Their Ability To Inhibit Entry of Human Immunodeficiency Virus Type 1

2005 ◽  
Vol 79 (3) ◽  
pp. 1930-1933 ◽  
Author(s):  
Xavier Carnec ◽  
Lan Quan ◽  
William C. Olson ◽  
Uriel Hazan ◽  
Tatjana Dragic
Keyword(s):  
Monoclonal Antibodies ◽  
Structure And Function ◽  
Cxcr4 Expression ◽  
Target Cells ◽  
Cell Type ◽  
Immunodeficiency Virus ◽  
Cell Type Specific ◽  
And Function ◽  
Hiv 1

ABSTRACT CXCR4 is one of two physiologically relevant human immunodeficiency type 1 (HIV-1) entry coreceptors. Studies of CXCR4 mutants have not clearly identified the determinants of coreceptor function and specificity. We therefore used a panel of monoclonal antibodies to further elucidate CXCR4 expression, structure, and function. Our findings show the existence of conformational subpopulations of CXCR4 that are in equilibrium on the cell surface but are not cell type specific as previously reported. HIV-1 X4 isolates can interact with multiple CXCR4 conformations in order to gain entry into target cells.

scholarly journals Expression and Function of Chemokine Receptors on Human Thymocytes: Implications for Infection by Human Immunodeficiency Virus Type 1

2001 ◽  
Vol 75 (18) ◽  
pp. 8752-8760 ◽  
Author(s):  
James R. Taylor ◽  
Katherine C. Kimbrell ◽  
Robert Scoggins ◽  
Marie Delaney ◽  
Lijun Wu ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Chemokine Receptors ◽  
Cross Reactivity ◽  
Immunodeficiency Virus ◽  
Chemokine Ligands ◽  
And Function ◽  
Hiv 1

ABSTRACT The presence or absence of the receptor CD4 and the coreceptors CCR5 and CXCR4 restrict the cell tropism of human immunodeficiency virus type 1 (HIV-1). Despite the importance of thymic infection by HIV-1, conflicting reports regarding the expression of HIV-1 coreceptors on human thymocytes have not been resolved. We assayed the expression and function of the major HIV-1 coreceptors, CCR5 and CXCR4, as well as CCR4 and CCR7 as controls, on human thymocytes. We detected CCR5 on 2.5% of thymocytes, CXCR4 on 53% of the cells, and CCR4 on 16% and CCR7 on 11% of human thymocytes. Moreover, infection by R5 HIV-1 did not significantly induce expression of CCR5. We found that two widely used anti-CCR5 monoclonal antibodies cross-reacted with CCR8, which may account for discrepancies among published reports of CCR5 expression on primary cells. This cross-reactivity could be eliminated by deletion of amino acids 2 through 4 of CCR8. Chemotaxis assays showed that SDF-1, which binds CXCR4; MDC, which binds CCR4; and ELC, which binds CCR7, mediated significant chemotaxis of thymocytes. In contrast, MIP-1β, whose receptor is CCR5, did not induce significant chemotaxis. Our results indicate that CXCR4, CCR4, CCR7, and their chemokine ligands may be involved in thymocyte migration during development in the thymus. CCR5 and its ligands, however, are likely not involved in these processes. Furthermore, the pattern of CCR5 and CXCR4 expression that we found may explain the greater susceptibility of human thymocytes to infection by HIV-1 isolates capable of using CXCR4 in cell entry compared to those that use only CCR5.

A Synthetic Peptide Derived From Human Immunodeficiency Virus Type 1 gp120 Downregulates the Expression and Function of Chemokine Receptors CCR5 and CXCR4 in Monocytes by Activating the 7-Transmembrane G-Protein–Coupled Receptor FPRL1/LXA4R

Blood ◽  
1999 ◽  
Vol 94 (4) ◽  
pp. 1165-1173 ◽  
Author(s):  
Xiyun Deng ◽  
Hirotsugu Ueda ◽  
Shao Bo Su ◽  
Wanghua Gong ◽  
Nancy M. Dunlop ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
G Protein ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Synthetic Peptide ◽  
Immunodeficiency Virus ◽  
And Function ◽  
G Protein Coupled ◽  
Hiv 1

Abstract Because envelope gp120 of various strains of human immunodeficiency virus type 1 (HIV-1) downregulates the expression and function of a variety of chemoattractant receptors through a process of heterologous desensitization, we investigated whether epitopes derived from gp120 could mimic the effect. A synthetic peptide domain, designated F peptide, corresponding to amino acid residues 414-434 in the V4-C4 region of gp120 of the HIV-1 Bru strain, potently reduced monocyte binding and chemotaxis response to macrophage inflammatory protein 1β (MIP-1β) and stromal cell-derived factor 1 (SDF-1), chemokines that use the receptors CCR5 and CXCR4, respectively. Further study showed that F peptide by itself is an inducer of chemotaxis and calcium mobilization in human monocytes and neutrophils. In cross-desensitization experiments, among the numerous chemoattractants tested, only the bacterial chemotactic peptide fMLF, when used at high concentrations, partially attenuated calcium mobilization induced by F peptide in phagocytes, suggesting that this peptide domain might share a 7-transmembrane, G-protein–coupled receptor with fMLF. By using cells transfected with cDNAs encoding receptors that interact with fMLF, we found that F peptide uses an fMLF receptor variant, FPRL1, as a functional receptor. The activation of monocytes by F peptide resulted in downregulation of the cell surface expression of CCR5 and CXCR4 in a protein kinase C-dependent manner. These results demonstrate that activation of FPRL1 on human moncytes by a peptide domain derived from HIV-1 gp120 could lead to desensitization of cell response to other chemoattractants. This may explain, at least in part, the initial activation of innate immune responses in HIV-1–infected patients followed by immune suppression.

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