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Papers by Jack Collins

Frontiers in Immunology

COVID-19 ranges from asymptomatic in 35% of cases to severe in 20% of patients. Differences in th... more COVID-19 ranges from asymptomatic in 35% of cases to severe in 20% of patients. Differences in the type and degree of inflammation appear to determine the severity of the disease. Recent reports show an increase in circulating monocytic-myeloid-derived suppressor cells (M-MDSC) in severe COVID 19 that deplete arginine but are not associated with respiratory complications. Our data shows that differences in the type, function and transcriptome of granulocytic-MDSC (G-MDSC) may in part explain the severity COVID-19, in particular the association with pulmonary complications. Large infiltrates by Arginase 1+ G-MDSC (Arg+G-MDSC), expressing NOX-1 and NOX-2 (important for production of reactive oxygen species) were found in the lungs of patients who died from COVID-19 complications. Increased circulating Arg+G-MDSC depleted arginine, which impaired T cell receptor and endothelial cell function. Transcriptomic signatures of G-MDSC from patients with different stages of COVID-19, revealed ...

J Am Chem Soc, 1991

Semiempirical, molecular mechanics, and molecular dynamics calculations have been performed to th... more Semiempirical, molecular mechanics, and molecular dynamics calculations have been performed to theoretically examine the metabolism of 2-n-propylpentanoic acid (valproic acid, VPA), a widely used therapeutic agent for the control of seizure disorders, by cytochrome P450. In particular, the stereospecificity and product distribution of the hydroxylated metabolites of VPA are predicted for the P450,, isozyme and compared to the experimental data from microsomal P450. Quantum mechanical results are consistent with hypothesized mechanisms for the formation of 2-n-propyl-4-pentenoic acid (4-ene-VPA), a hepatotoxic metabolite, by a P450-catalyzed dehydrogenation reaction. The current theoretical results suggest that differences in the binding sites between mammalian P450 isozymes and P450,, may modulate the product distribution via steric interactions with the substrate.

J Am Chem Soc, 1991

... (c) Brauer, H.-D.; Stieger, H.; Hyde, J. S.; Kispert, LD; Luckhurst, GR Mol. Phys. 1%9, 17, 4... more ... (c) Brauer, H.-D.; Stieger, H.; Hyde, J. S.; Kispert, LD; Luckhurst, GR Mol. Phys. 1%9, 17, 457. ... Department of Pharmaceutical Chemistry School of Pharmacy, University of California San Francisco, California 941 43-0446 Jack R. Collins,* Debra L. Camper, and Gilda H. Loew* ...

Int J Quantum Chem, 1988

ABSTRACT

Nature Struct Biology, 1995

J Am Chem Soc, 1994

Cytochrome P450 enzymes catalyze three general classes of oxidative reactions: n-bond epoxidation... more Cytochrome P450 enzymes catalyze three general classes of oxidative reactions: n-bond epoxidations, heteroatom (N, S, P) oxidations, and carbon hydroxylations. Recent work has shown that cytochrome P450,, (CYP101) enantioselectively oxidizes styrene and p-methylstyrene and that molecular dynamics calculations predict the enantiomeric specificity with remarkable accuracy. Cytochrome P45OCa, is shown here to also catalyze the stereoselective sulfoxidation of thioanisole (R:S 72:28) and p-methylthioanisole (R:S 4852). Molecular dynamics calculations suggest that oxidations of thioanisole and p-methylthioanisole by cytochrome P450,, should yield the corresponding sulfoxides in R:S ratios of 65:35 and 22:78, respectively. The predicted and experimental enantiomer ratios for thioanisole change in a similar manner when a p-methyl substituent is added to the thioanisole. The theoretical treatment correctly predicts the experimental finding that a p-methyl group inverts the preferred sulfoxide stereochemistry.

Theochem, Jan 30, 2008

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 protein... more Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pKa values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photophysical properties of these proteins. The pKa values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df,2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d,p) calculations of solvation energies. The results show that the pKa's of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.

ACS Symposium Series, 1989

Page 1. Chapter 24 Ground-State Properties of Heme Complexes in Model Compounds and Intact Protei... more Page 1. Chapter 24 Ground-State Properties of Heme Complexes in Model Compounds and Intact Proteins Frank U. Axe1, Lek Chantranupong1, Ahmad Waleh1, Jack Collins2, and Gilda H. Loew2 1The Rockefeller University ...

We present an analysis framework to assess the quality and accuracy of vessel segmentation algori... more We present an analysis framework to assess the quality and accuracy of vessel segmentation algorithms for three dimensional images. We generate synthetic (in silico) vessel models which act as ground truth and are constructed to embody varying morphological features. These models are transformed into images constructed under different levels of contrast, noise, and intensity. To demonstrate the use of our framework, we implemented two segmentation algorithms and compare the results to the ground truth model using several measures to quantify the accuracy and quality of segmentation. Furthermore, we collect metrics which describe the characteristics of the vessels it fails to segment. Our approach is illustrated with several examples. Funded by NCI Contract No.HHSN261200800001E.

Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications II, 2010

ABSTRACT Modern molecular modeling tools are intensively used to gain knowledge of events occurri... more ABSTRACT Modern molecular modeling tools are intensively used to gain knowledge of events occurring upon photoexcitation of organic chromophores in the gas-phase, in solution and in protein matrices. We applied quantum mechanical approach to estimate equilibrium geometry configurations as well as positions and intensities of spectral bands for a number of red fluorescent proteins, including the DsRed from Discosoma coral, and its mutants of the so-called mFruits series. As demonstrated in our previous simulations for GFP and blue fluorescent proteins, this strategy was proven to be productive for modeling. The model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. Mechanisms of photoexcitation, identification of the functional states of the chromophores, elucidation the role of point mutations in the photoreceptor proteins are considered on the basis of simulations.

Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications III, 2011

ABSTRACT Modern computational approaches based on quantum mechanical methods to characterize stru... more ABSTRACT Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in proteins are intensively used to gain knowledge of events occurring upon of their photoexcitation. Primary attention is paid to the species from the family of the green fluorescent protein applied as biomarkers in living cells. We apply quantum chemical approaches for accurate calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S0-S1 optical transitions of the intriguing kindling protein asFP595. Its precursor, the chromoprotein asCP from the sea anemony Anemonia sulcata is characterized by distinctive spectral properties: at low light intensities the wild-type protein is weakly fluorescent with the very low quantum yield, however, high intensity irradiation with green light leads to a drastic increase of quantum yield. This phenomenon is now termed "kindling". In simulations, the model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies and applications of this fluorescent protein.

Biophysical journal, Jan 6, 2015

The orientation factor κ(2), one of the key parameters defining Förster resonance energy transfer... more The orientation factor κ(2), one of the key parameters defining Förster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S0,min → S1 excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S1,min → S0 emission for TagRFP. These data allowed us to estimate κ(2) values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.

Genome biology, 2007

The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomer... more The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomeration algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules. This organization is accomplished by mining the complex biological co-occurrences found in multiple sources of functional annotation. It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context.

Origins of Life and Evolution of the Biosphere, 1986

Nucleic Acids Research, 2013

The non-B DB, available at http://nonb.abcc.ncifcrf .gov, catalogs predicted non-B DNA-forming se... more The non-B DB, available at http://nonb.abcc.ncifcrf .gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

Frontiers in Immunology

COVID-19 ranges from asymptomatic in 35% of cases to severe in 20% of patients. Differences in th... more COVID-19 ranges from asymptomatic in 35% of cases to severe in 20% of patients. Differences in the type and degree of inflammation appear to determine the severity of the disease. Recent reports show an increase in circulating monocytic-myeloid-derived suppressor cells (M-MDSC) in severe COVID 19 that deplete arginine but are not associated with respiratory complications. Our data shows that differences in the type, function and transcriptome of granulocytic-MDSC (G-MDSC) may in part explain the severity COVID-19, in particular the association with pulmonary complications. Large infiltrates by Arginase 1+ G-MDSC (Arg+G-MDSC), expressing NOX-1 and NOX-2 (important for production of reactive oxygen species) were found in the lungs of patients who died from COVID-19 complications. Increased circulating Arg+G-MDSC depleted arginine, which impaired T cell receptor and endothelial cell function. Transcriptomic signatures of G-MDSC from patients with different stages of COVID-19, revealed ...

J Am Chem Soc, 1991

Semiempirical, molecular mechanics, and molecular dynamics calculations have been performed to th... more Semiempirical, molecular mechanics, and molecular dynamics calculations have been performed to theoretically examine the metabolism of 2-n-propylpentanoic acid (valproic acid, VPA), a widely used therapeutic agent for the control of seizure disorders, by cytochrome P450. In particular, the stereospecificity and product distribution of the hydroxylated metabolites of VPA are predicted for the P450,, isozyme and compared to the experimental data from microsomal P450. Quantum mechanical results are consistent with hypothesized mechanisms for the formation of 2-n-propyl-4-pentenoic acid (4-ene-VPA), a hepatotoxic metabolite, by a P450-catalyzed dehydrogenation reaction. The current theoretical results suggest that differences in the binding sites between mammalian P450 isozymes and P450,, may modulate the product distribution via steric interactions with the substrate.

J Am Chem Soc, 1991

... (c) Brauer, H.-D.; Stieger, H.; Hyde, J. S.; Kispert, LD; Luckhurst, GR Mol. Phys. 1%9, 17, 4... more ... (c) Brauer, H.-D.; Stieger, H.; Hyde, J. S.; Kispert, LD; Luckhurst, GR Mol. Phys. 1%9, 17, 457. ... Department of Pharmaceutical Chemistry School of Pharmacy, University of California San Francisco, California 941 43-0446 Jack R. Collins,* Debra L. Camper, and Gilda H. Loew* ...

Int J Quantum Chem, 1988

ABSTRACT

Nature Struct Biology, 1995

J Am Chem Soc, 1994

Cytochrome P450 enzymes catalyze three general classes of oxidative reactions: n-bond epoxidation... more Cytochrome P450 enzymes catalyze three general classes of oxidative reactions: n-bond epoxidations, heteroatom (N, S, P) oxidations, and carbon hydroxylations. Recent work has shown that cytochrome P450,, (CYP101) enantioselectively oxidizes styrene and p-methylstyrene and that molecular dynamics calculations predict the enantiomeric specificity with remarkable accuracy. Cytochrome P45OCa, is shown here to also catalyze the stereoselective sulfoxidation of thioanisole (R:S 72:28) and p-methylthioanisole (R:S 4852). Molecular dynamics calculations suggest that oxidations of thioanisole and p-methylthioanisole by cytochrome P450,, should yield the corresponding sulfoxides in R:S ratios of 65:35 and 22:78, respectively. The predicted and experimental enantiomer ratios for thioanisole change in a similar manner when a p-methyl substituent is added to the thioanisole. The theoretical treatment correctly predicts the experimental finding that a p-methyl group inverts the preferred sulfoxide stereochemistry.

Theochem, Jan 30, 2008

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 protein... more Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pKa values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photophysical properties of these proteins. The pKa values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df,2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d,p) calculations of solvation energies. The results show that the pKa's of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.

ACS Symposium Series, 1989

Page 1. Chapter 24 Ground-State Properties of Heme Complexes in Model Compounds and Intact Protei... more Page 1. Chapter 24 Ground-State Properties of Heme Complexes in Model Compounds and Intact Proteins Frank U. Axe1, Lek Chantranupong1, Ahmad Waleh1, Jack Collins2, and Gilda H. Loew2 1The Rockefeller University ...

We present an analysis framework to assess the quality and accuracy of vessel segmentation algori... more We present an analysis framework to assess the quality and accuracy of vessel segmentation algorithms for three dimensional images. We generate synthetic (in silico) vessel models which act as ground truth and are constructed to embody varying morphological features. These models are transformed into images constructed under different levels of contrast, noise, and intensity. To demonstrate the use of our framework, we implemented two segmentation algorithms and compare the results to the ground truth model using several measures to quantify the accuracy and quality of segmentation. Furthermore, we collect metrics which describe the characteristics of the vessels it fails to segment. Our approach is illustrated with several examples. Funded by NCI Contract No.HHSN261200800001E.

Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications II, 2010

ABSTRACT Modern molecular modeling tools are intensively used to gain knowledge of events occurri... more ABSTRACT Modern molecular modeling tools are intensively used to gain knowledge of events occurring upon photoexcitation of organic chromophores in the gas-phase, in solution and in protein matrices. We applied quantum mechanical approach to estimate equilibrium geometry configurations as well as positions and intensities of spectral bands for a number of red fluorescent proteins, including the DsRed from Discosoma coral, and its mutants of the so-called mFruits series. As demonstrated in our previous simulations for GFP and blue fluorescent proteins, this strategy was proven to be productive for modeling. The model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. Mechanisms of photoexcitation, identification of the functional states of the chromophores, elucidation the role of point mutations in the photoreceptor proteins are considered on the basis of simulations.

Reporters, Markers, Dyes, Nanoparticles, and Molecular Probes for Biomedical Applications III, 2011

ABSTRACT Modern computational approaches based on quantum mechanical methods to characterize stru... more ABSTRACT Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in proteins are intensively used to gain knowledge of events occurring upon of their photoexcitation. Primary attention is paid to the species from the family of the green fluorescent protein applied as biomarkers in living cells. We apply quantum chemical approaches for accurate calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S0-S1 optical transitions of the intriguing kindling protein asFP595. Its precursor, the chromoprotein asCP from the sea anemony Anemonia sulcata is characterized by distinctive spectral properties: at low light intensities the wild-type protein is weakly fluorescent with the very low quantum yield, however, high intensity irradiation with green light leads to a drastic increase of quantum yield. This phenomenon is now termed "kindling". In simulations, the model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies and applications of this fluorescent protein.

Biophysical journal, Jan 6, 2015

The orientation factor κ(2), one of the key parameters defining Förster resonance energy transfer... more The orientation factor κ(2), one of the key parameters defining Förster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S0,min → S1 excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S1,min → S0 emission for TagRFP. These data allowed us to estimate κ(2) values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.

Genome biology, 2007

The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomer... more The DAVID Gene Functional Classification Tool http://david.abcc.ncifcrf.gov uses a novel agglomeration algorithm to condense a list of genes or associated biological terms into organized classes of related genes or biology, called biological modules. This organization is accomplished by mining the complex biological co-occurrences found in multiple sources of functional annotation. It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context.

Origins of Life and Evolution of the Biosphere, 1986

Nucleic Acids Research, 2013

The non-B DB, available at http://nonb.abcc.ncifcrf .gov, catalogs predicted non-B DNA-forming se... more The non-B DB, available at http://nonb.abcc.ncifcrf .gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.