Jyotica Batra | Mayo Clinic (original) (raw)

Papers by Jyotica Batra

Charged residues play important roles in the folding of proteins and their interactions with biol... more Charged residues play important roles in the folding of proteins and their interactions with biological targets. We have developed computational models for predicting electrostatic contributions to protein folding and binding stability. To rigorously test and further refine these models, we carried out experimental studies on the effects of charge mutations on the folding stability of FKBP. Two close homologues of FKBP, FKBP12 and FKBP12. 6, differ in 18 of 107 positions, and 8 of which involve substitutions of charged residues. These 8 ...

Cancer Research, 2013

ABSTRACT Abstract: Matrix metalloproteinases (MMPs), a family of extracellular matrix degrading p... more ABSTRACT Abstract: Matrix metalloproteinases (MMPs), a family of extracellular matrix degrading proteins, have been found to be upregulated in many human cancers and have been shown to contribute to cancer progression. There have been many aborted attempts to target MMPs therapeutically using small molecule inhibitors; the limited selectivity of most MMP inhibitors may be a major factor contributing to their poor effectiveness. As an alternative to small molecule MMP inhibitors, we are developing new methodology to create selective protein inhibitors of MMPs, based on the scaffold of the natural inhibitor TIMP-1, that may be used as protein therapeutics. Because TIMP-1 has a very short plasma half-life, we have developed methods for PEGylation that extend the plasma half-life to about 24h while preserving MMP inhibitory activity, rendering it more suitable for in vivo applications. We have also generated mutations in TIMP-1 that confer selective binding toward particular MMPs. The targets thus far pursued include MMP-9, MMP-3, and MMP-10, which represent therapeutic targets of interest in breast cancer and lung cancer. In the future, the methods developed here can be used to identify TIMP-1 variants selective toward additional MMPs, which may be of utility in the research and treatment of many human cancers.

Encyclopedia of Inorganic and Bioinorganic Chemistry, 2011

Biophysical Journal, 2009

Macromolecular crowding has long been known to significantly affect protein oligomerization, and ... more Macromolecular crowding has long been known to significantly affect protein oligomerization, and yet no direct quantitative measurements appear to have been made of its effects on the binding free energy of the elemental step of adding a single subunit. Here, we report the effects of two crowding agents on the binding free energy of two subunits in the Escherichia coli polymerase III holoenzyme. The crowding agents are found, paradoxically, to have only a modest stabilizing effect, of the order of 1 kcal/mol, on the binding of the two subunits. Systematic variations in the level of stabilization with crowder size are nevertheless observed. The data are consistent with theoretical predictions based on atomistic modeling of excluded-volume interactions with crowders. We reconcile the apparent paradox presented by our data by noting that the modest effects of crowding on elemental binding steps are cumulative, and thus lead to substantial stabilization of higher oligomers. Correspondingly, the effects of small variations in the level of crowding during the lifetime of a cell may be magnified, suggesting that crowding may play a role in increased susceptibility to protein aggregation-related diseases with aging.

Blood-brain barrier (BBB) dysfunction in acute liver failure (ALF) results in increased BBB perme... more Blood-brain barrier (BBB) dysfunction in acute liver failure (ALF) results in increased BBB permeability that often precludes the patients from obtaining a life-saving liver transplantation. It remains controversial whether matrix metalloproteinase-9 (MMP-9) from the injured liver contributes to the deregulation of BBB function in ALF. We selectively upregulated a physiologic inhibitor of MMP-9 (TIMP-1) with a single intracerebroventricular injection of TIMP-1 cDNA plasmids at 48 and 72 hours, or with pegylated-TIMP-1 protein. Acute liver failure was induced with tumor necrosis factor-a and D-( þ )-galactosamine in mice. Permeability of BBB was assessed with sodium fluorescein (NaF) extravasation. We found a significant increase in TIMP-1 within the central nervous system (CNS) after the administration of TIMP-1 cDNA plasmids and that increased TIMP-1 within the CNS resulted in an attenuation of BBB permeability, a reduction in activation of epidermal growth factor receptor and p38 mitogen-activated protein kinase signals, and a restoration of the tight junction protein occludin in mice with experimental ALF. Pegylated TIMP-1 provided similar protection against BBB permeability in mice with ALF. Our results provided a proof of principle that MMP-9 contributes to the BBB dysfunction in ALF and suggests a potential therapeutic role of TIMP-1 in ALF.

Abstract Interactions between charged residues are known to have significant effects on protein f... more Abstract Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent interactions are altered by mutating one or more residues, resulting in change in the protein stability to considerable extent. The main goal of this dissertation is to understand contributions, specifically from electrostatic interactions, to the protein folding stability and also, to devise strategies in order to enhance protein stability.

Abstract Interactions between charged residues are known to have significant effects on protein f... more Abstract Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent interactions are altered by mutating one or more residues, resulting in change in the protein stability to considerable extent. The main goal of this dissertation is to understand contributions, specifically from electrostatic interactions, to the protein folding stability and also, to devise strategies in order to enhance protein stability.

Background: Chymotrypsin C (CTRC) targets specific regulatory cleavage sites within trypsinogens ... more Background: Chymotrypsin C (CTRC) targets specific regulatory cleavage sites within trypsinogens and procarboxypeptidases. Results: The crystal structure of CTRC reveals the structural basis of substrate specificity. Conclusion: Long-range electrostatic and hydrophobic complementarity drives CTRC association with preferred substrates. Significance: The observations reveal the mechanistic basis for CTRC selectivity in digestive enzyme activation and degradation.

Excess proteolytic activity of matrix metalloproteinases (MMPs) contributes to the development of... more Excess proteolytic activity of matrix metalloproteinases (MMPs) contributes to the development of arthritis, cardiovascular diseases and cancer progression, implicating these enzymes as therapeutic targets. While many small molecule inhibitors of MMPs have been developed, clinical uses have been limited, in part by toxicity and off-target effects. Development of the endogenous tissue inhibitors of metalloproteinases (TIMPs) as recombinant biopharmaceuticals represents an alternative therapeutic approach; however, the short plasma half-life of recombinant TIMPs has restricted their potential in this arena. To overcome this limitation, we have modified recombinant human TIMP-1 (rhTIMP-1) by PEGylation on lysine residues. We analyzed a mixture of mono-and di-PEGylated rhTIMP-1 species modified by attachment of 20 kDa mPEG chains (PEG 20K -TIMP-1), as confirmed by SELDI-TOF mass spectrometry. This preparation retained complete inhibitory activity toward the MMP-3 catalytic domain and partial inhibitory activity toward full length MMP-9. Pharmacokinetic evaluation showed that PEGylation extended the plasma half-life of rhTIMP-1 in mice from 1.1 h to 28 h. In biological assays, PEG 20K -TIMP-1 inhibited both MMP-dependent cancer cell invasion and tumor cell associated gelatinase activity. Overall these results suggest that PEGylated TIMP-1 exhibits improved potential for development as an anti-cancer recombinant protein therapeutic, and additionally may offer potential for clinical applications in the treatment of other diseases.

Matrix metalloproteinases (Mmps) stimulate tumor invasion and metastasis by degrading the extrace... more Matrix metalloproteinases (Mmps) stimulate tumor invasion and metastasis by degrading the extracellular matrix. Here we reveal an unexpected role for Mmp10 (stromelysin 2) in the maintenance and tumorigenicity of mouse lung cancer stemlike cells (CSC). Mmp10 is highly expressed in oncosphere cultures enriched in CSCs and RNAi-mediated knockdown of Mmp10 leads to a loss of stem cell marker gene expression and inhibition of oncosphere growth, clonal expansion, and transformed growth in vitro. Interestingly, clonal expansion of Mmp10 deficient oncospheres can be restored by addition of exogenous Mmp10 protein to the culture medium, demonstrating a direct role for Mmp10 in the proliferation of these cells. Oncospheres exhibit enhanced tumor-initiating and metastatic activity when injected orthotopically into syngeneic mice, whereas Mmp10-deficient cultures show a severe defect in tumor initiation. Conversely, oncospheres implanted into syngeneic non-transgenic or Mmp10 2/2 mice show no significant difference in tumor initiation, growth or metastasis, demonstrating the importance of Mmp10 produced by cancer cells rather than the tumor microenvironment in lung tumor initiation and maintenance. Analysis of gene expression data from human cancers reveals a strong positive correlation between tumor Mmp10 expression and metastatic behavior in many human tumor types. Thus, Mmp10 is required for maintenance of a highly tumorigenic, cancer-initiating, metastatic stem-like cell population in lung cancer. Our data demonstrate for the first time that Mmp10 is a critical lung cancer stem cell gene and novel therapeutic target for lung cancer stem cells.

Background: Stromelysins MMP-3 and MMP-10 serve distinct functions, and differential inhibition b... more Background: Stromelysins MMP-3 and MMP-10 serve distinct functions, and differential inhibition by TIMPs offers one mechanism of control.

Proteins: Structure, Function, and …, Jan 1, 2009

Biophysical Journal, Jan 1, 2009

Charged residues play important roles in the folding of proteins and their interactions with biol... more Charged residues play important roles in the folding of proteins and their interactions with biological targets. We have developed computational models for predicting electrostatic contributions to protein folding and binding stability. To rigorously test and further refine these models, we carried out experimental studies on the effects of charge mutations on the folding stability of FKBP. Two close homologues of FKBP, FKBP12 and FKBP12. 6, differ in 18 of 107 positions, and 8 of which involve substitutions of charged residues. These 8 ...

Cancer Research, 2013

ABSTRACT Abstract: Matrix metalloproteinases (MMPs), a family of extracellular matrix degrading p... more ABSTRACT Abstract: Matrix metalloproteinases (MMPs), a family of extracellular matrix degrading proteins, have been found to be upregulated in many human cancers and have been shown to contribute to cancer progression. There have been many aborted attempts to target MMPs therapeutically using small molecule inhibitors; the limited selectivity of most MMP inhibitors may be a major factor contributing to their poor effectiveness. As an alternative to small molecule MMP inhibitors, we are developing new methodology to create selective protein inhibitors of MMPs, based on the scaffold of the natural inhibitor TIMP-1, that may be used as protein therapeutics. Because TIMP-1 has a very short plasma half-life, we have developed methods for PEGylation that extend the plasma half-life to about 24h while preserving MMP inhibitory activity, rendering it more suitable for in vivo applications. We have also generated mutations in TIMP-1 that confer selective binding toward particular MMPs. The targets thus far pursued include MMP-9, MMP-3, and MMP-10, which represent therapeutic targets of interest in breast cancer and lung cancer. In the future, the methods developed here can be used to identify TIMP-1 variants selective toward additional MMPs, which may be of utility in the research and treatment of many human cancers.

Encyclopedia of Inorganic and Bioinorganic Chemistry, 2011

Biophysical Journal, 2009

Macromolecular crowding has long been known to significantly affect protein oligomerization, and ... more Macromolecular crowding has long been known to significantly affect protein oligomerization, and yet no direct quantitative measurements appear to have been made of its effects on the binding free energy of the elemental step of adding a single subunit. Here, we report the effects of two crowding agents on the binding free energy of two subunits in the Escherichia coli polymerase III holoenzyme. The crowding agents are found, paradoxically, to have only a modest stabilizing effect, of the order of 1 kcal/mol, on the binding of the two subunits. Systematic variations in the level of stabilization with crowder size are nevertheless observed. The data are consistent with theoretical predictions based on atomistic modeling of excluded-volume interactions with crowders. We reconcile the apparent paradox presented by our data by noting that the modest effects of crowding on elemental binding steps are cumulative, and thus lead to substantial stabilization of higher oligomers. Correspondingly, the effects of small variations in the level of crowding during the lifetime of a cell may be magnified, suggesting that crowding may play a role in increased susceptibility to protein aggregation-related diseases with aging.

Blood-brain barrier (BBB) dysfunction in acute liver failure (ALF) results in increased BBB perme... more Blood-brain barrier (BBB) dysfunction in acute liver failure (ALF) results in increased BBB permeability that often precludes the patients from obtaining a life-saving liver transplantation. It remains controversial whether matrix metalloproteinase-9 (MMP-9) from the injured liver contributes to the deregulation of BBB function in ALF. We selectively upregulated a physiologic inhibitor of MMP-9 (TIMP-1) with a single intracerebroventricular injection of TIMP-1 cDNA plasmids at 48 and 72 hours, or with pegylated-TIMP-1 protein. Acute liver failure was induced with tumor necrosis factor-a and D-( þ )-galactosamine in mice. Permeability of BBB was assessed with sodium fluorescein (NaF) extravasation. We found a significant increase in TIMP-1 within the central nervous system (CNS) after the administration of TIMP-1 cDNA plasmids and that increased TIMP-1 within the CNS resulted in an attenuation of BBB permeability, a reduction in activation of epidermal growth factor receptor and p38 mitogen-activated protein kinase signals, and a restoration of the tight junction protein occludin in mice with experimental ALF. Pegylated TIMP-1 provided similar protection against BBB permeability in mice with ALF. Our results provided a proof of principle that MMP-9 contributes to the BBB dysfunction in ALF and suggests a potential therapeutic role of TIMP-1 in ALF.

Abstract Interactions between charged residues are known to have significant effects on protein f... more Abstract Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent interactions are altered by mutating one or more residues, resulting in change in the protein stability to considerable extent. The main goal of this dissertation is to understand contributions, specifically from electrostatic interactions, to the protein folding stability and also, to devise strategies in order to enhance protein stability.

Abstract Interactions between charged residues are known to have significant effects on protein f... more Abstract Interactions between charged residues are known to have significant effects on protein folding stability and binding properties. The contributions of different types of non-covalent interactions are altered by mutating one or more residues, resulting in change in the protein stability to considerable extent. The main goal of this dissertation is to understand contributions, specifically from electrostatic interactions, to the protein folding stability and also, to devise strategies in order to enhance protein stability.

Background: Chymotrypsin C (CTRC) targets specific regulatory cleavage sites within trypsinogens ... more Background: Chymotrypsin C (CTRC) targets specific regulatory cleavage sites within trypsinogens and procarboxypeptidases. Results: The crystal structure of CTRC reveals the structural basis of substrate specificity. Conclusion: Long-range electrostatic and hydrophobic complementarity drives CTRC association with preferred substrates. Significance: The observations reveal the mechanistic basis for CTRC selectivity in digestive enzyme activation and degradation.

Excess proteolytic activity of matrix metalloproteinases (MMPs) contributes to the development of... more Excess proteolytic activity of matrix metalloproteinases (MMPs) contributes to the development of arthritis, cardiovascular diseases and cancer progression, implicating these enzymes as therapeutic targets. While many small molecule inhibitors of MMPs have been developed, clinical uses have been limited, in part by toxicity and off-target effects. Development of the endogenous tissue inhibitors of metalloproteinases (TIMPs) as recombinant biopharmaceuticals represents an alternative therapeutic approach; however, the short plasma half-life of recombinant TIMPs has restricted their potential in this arena. To overcome this limitation, we have modified recombinant human TIMP-1 (rhTIMP-1) by PEGylation on lysine residues. We analyzed a mixture of mono-and di-PEGylated rhTIMP-1 species modified by attachment of 20 kDa mPEG chains (PEG 20K -TIMP-1), as confirmed by SELDI-TOF mass spectrometry. This preparation retained complete inhibitory activity toward the MMP-3 catalytic domain and partial inhibitory activity toward full length MMP-9. Pharmacokinetic evaluation showed that PEGylation extended the plasma half-life of rhTIMP-1 in mice from 1.1 h to 28 h. In biological assays, PEG 20K -TIMP-1 inhibited both MMP-dependent cancer cell invasion and tumor cell associated gelatinase activity. Overall these results suggest that PEGylated TIMP-1 exhibits improved potential for development as an anti-cancer recombinant protein therapeutic, and additionally may offer potential for clinical applications in the treatment of other diseases.

Matrix metalloproteinases (Mmps) stimulate tumor invasion and metastasis by degrading the extrace... more Matrix metalloproteinases (Mmps) stimulate tumor invasion and metastasis by degrading the extracellular matrix. Here we reveal an unexpected role for Mmp10 (stromelysin 2) in the maintenance and tumorigenicity of mouse lung cancer stemlike cells (CSC). Mmp10 is highly expressed in oncosphere cultures enriched in CSCs and RNAi-mediated knockdown of Mmp10 leads to a loss of stem cell marker gene expression and inhibition of oncosphere growth, clonal expansion, and transformed growth in vitro. Interestingly, clonal expansion of Mmp10 deficient oncospheres can be restored by addition of exogenous Mmp10 protein to the culture medium, demonstrating a direct role for Mmp10 in the proliferation of these cells. Oncospheres exhibit enhanced tumor-initiating and metastatic activity when injected orthotopically into syngeneic mice, whereas Mmp10-deficient cultures show a severe defect in tumor initiation. Conversely, oncospheres implanted into syngeneic non-transgenic or Mmp10 2/2 mice show no significant difference in tumor initiation, growth or metastasis, demonstrating the importance of Mmp10 produced by cancer cells rather than the tumor microenvironment in lung tumor initiation and maintenance. Analysis of gene expression data from human cancers reveals a strong positive correlation between tumor Mmp10 expression and metastatic behavior in many human tumor types. Thus, Mmp10 is required for maintenance of a highly tumorigenic, cancer-initiating, metastatic stem-like cell population in lung cancer. Our data demonstrate for the first time that Mmp10 is a critical lung cancer stem cell gene and novel therapeutic target for lung cancer stem cells.

Background: Stromelysins MMP-3 and MMP-10 serve distinct functions, and differential inhibition b... more Background: Stromelysins MMP-3 and MMP-10 serve distinct functions, and differential inhibition by TIMPs offers one mechanism of control.

Proteins: Structure, Function, and …, Jan 1, 2009

Biophysical Journal, Jan 1, 2009