IU Indianapolis ScholarWorks :: Browsing by Author "Liu, Ming"

Browsing by Author "Liu, Ming"

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Biosynthesis, structure, and folding of the insulin precursor protein
(Wiley, 2018-09) Liu, Ming; Weiss, Michael A.; Arunagiri, Anoop; Yong, Jing; Rege, Nischay; Sun, Jinhong; Haataja, Leena; Kaufman, Randal J.; Arvan, Peter; Biochemistry and Molecular Biology, School of Medicine
Insulin synthesis in pancreatic β-cells is initiated as preproinsulin. Prevailing glucose concentrations, which oscillate pre- and postprandially, exert major dynamic variation in preproinsulin biosynthesis. Accompanying upregulated translation of the insulin precursor includes elements of the endoplasmic reticulum (ER) translocation apparatus linked to successful orientation of the signal peptide, translocation and signal peptide cleavage of preproinsulin-all of which are necessary to initiate the pathway of proper proinsulin folding. Evolutionary pressures on the primary structure of proinsulin itself have preserved the efficiency of folding ("foldability"), and remarkably, these evolutionary pressures are distinct from those protecting the ultimate biological activity of insulin. Proinsulin foldability is manifest in the ER, in which the local environment is designed to assist in the overall load of proinsulin folding and to favour its disulphide bond formation (while limiting misfolding), all of which is closely tuned to ER stress response pathways that have complex (beneficial, as well as potentially damaging) effects on pancreatic β-cells. Proinsulin misfolding may occur as a consequence of exuberant proinsulin biosynthetic load in the ER, proinsulin coding sequence mutations, or genetic predispositions that lead to an altered ER folding environment. Proinsulin misfolding is a phenotype that is very much linked to deficient insulin production and diabetes, as is seen in a variety of contexts: rodent models bearing proinsulin-misfolding mutants, human patients with Mutant INS-gene-induced Diabetes of Youth (MIDY), animal models and human patients bearing mutations in critical ER resident proteins, and, quite possibly, in more common variety type 2 diabetes.
Deep Learning of Biomechanical Dynamics With Spatial Variability Mining and Model Sparsifiation
(2024-08) Liu, Ming; Zhang, Qingxue; King, Brian S.; Ben-Miled, Zina; Xia, Yuni
Deep learning of biomechanical dynamics is of great promise in smart health and data-driven precision medicine. Biomechanical dynamics are related to the movement patterns and gait characteristics of human people and may provide important insights if mined by deep learning models. However, efficient deep learning of biomechanical dynamics is still challenging, considering that there is a high diversity in the dynamics from different body locations, and the deep learning model may need to be lightweight enough to be able to be deployed in real-time. Targeting these challenges, we have firstly conducted studies on the spatial variability of biomechanical dynamics, aiming to evaluate and determine the optimal body location that is of great promise in robust physical activity type detection. Further, we have developed a framework for deep learning pruning, aiming to determine the optimal pruning schemes while maintaining acceptable performance. More specifically, the proposed approach first evaluates the layer importance of the deep learning model, and then leverages the probabilistic distribution-enabled threshold determination to optimize the pruning rate. The weighted random thresholding method is first investigated to further the understanding of the behavior of the pruning action for each layer. Afterwards, the Gaussian-based thresholding is designed to more effectively optimize the pruning strategies, which can find out the fine-grained pruning schemes with both emphasis and diversity regulation. Even further, we have enhanced and boosted the efficient deep learning framework, to co-optimize the accuracy and the continuity during the pruning process, with the latter metric – continuity meaning that the pruning locations in the weight matrices are encouraged to not cause too many noncontinuous non-pruned locations thereby achieving friendly model implementation. More specifically, the proposed framework leverages the significance scoring and the continuity scoring to quantize the characteristics of each of pruned convolutional filters, then leverages the clustering technique to group the pruned filters for each convolutional stage. Afterwards, the regularized ranking approach is designed to rank the pruned filters, through putting more emphasis on the continuity scores to encourage friendly implementation. In the end, a dual-thresholding strategy is leveraged to increase the diversity in this framework, during significance & continuity co-optimization. Experimental results have demonstrated promising findings, with enhanced understanding of the spatial variability of the biomechanical dynamics and best performance body location selection, with the effective deep learning model pruning framework that can reduce the model size significantly with performance maintained, and further, with the boosted framework that co-optimizes the accuracy and continuity to all consider the friendly implementation during the pruning process. Overall, this research will greatly advance the deep biomechanical mining towards efficient smart health.
Distinct states of proinsulin misfolding in MIDY
(Springer, 2021-08) Haataja, Leena; Arunagiri, Anoop; Hassan, Anis; Regan, Kaitlin; Tsai, Billy; Dhayalan, Balamurugan; Weiss, Michael A.; Liu, Ming; Arvan, Peter; Biochemistry and Molecular Biology, School of Medicine
A precondition for efficient proinsulin export from the endoplasmic reticulum (ER) is that proinsulin meets ER quality control folding requirements, including formation of the Cys(B19)-Cys(A20) "interchain" disulfide bond, facilitating formation of the Cys(B7)-Cys(A7) bridge. The third proinsulin disulfide, Cys(A6)-Cys(A11), is not required for anterograde trafficking, i.e., a "lose-A6/A11" mutant [Cys(A6), Cys(A11) both converted to Ser] is well secreted. Nevertheless, an unpaired Cys(A11) can participate in disulfide mispairings, causing ER retention of proinsulin. Among the many missense mutations causing the syndrome of Mutant INS gene-induced Diabetes of Youth (MIDY), all seem to exhibit perturbed proinsulin disulfide bond formation. Here, we have examined a series of seven MIDY mutants [including G(B8)V, Y(B26)C, L(A16)P, H(B5)D, V(B18)A, R(Cpep + 2)C, E(A4)K], six of which are essentially completely blocked in export from the ER in pancreatic β-cells. Three of these mutants, however, must disrupt the Cys(A6)-Cys(A11) pairing to expose a critical unpaired cysteine thiol perturbation of proinsulin folding and ER export, because when introduced into the proinsulin lose-A6/A11 background, these mutants exhibit native-like disulfide bonding and improved trafficking. This maneuver also ameliorates dominant-negative blockade of export of co-expressed wild-type proinsulin. A growing molecular understanding of proinsulin misfolding may permit allele-specific pharmacological targeting for some MIDY mutants.
Evolution of insulin at the edge of foldability and its medical implications
(National Academy of Sciences, 2020-11-24) Rege, Nischay K.; Liu, Ming; Yang, Yanwu; Dhayalan, Balamurugan; Wickramasinghe, Nalinda P.; Chen, Yen-Shan; Rahimi, Leili; Guo, Huan; Haataja, Leena; Sun, Jinhong; Ismail-Beigi, Faramarz; Phillips, Nelson B.; Arvan, Peter; Weiss, Michael A.; Biochemistry and Molecular Biology, School of Medicine
Proteins have evolved to be foldable, and yet determinants of foldability may be inapparent once the native state is reached. Insight has emerged from studies of diseases of protein misfolding, exemplified by monogenic diabetes mellitus due to mutations in proinsulin leading to endoplasmic reticulum stress and β-cell death. Cellular foldability of human proinsulin requires an invariant Phe within a conserved crevice at the receptor-binding surface (position B24). Any substitution, even related aromatic residue TyrB24, impairs insulin biosynthesis and secretion. As a seeming paradox, a monomeric TyrB24 insulin analog exhibits a native-like structure in solution with only a modest decrement in stability. Packing of TyrB24 is similar to that of PheB24, adjoining core cystine B19-A20 to seal the core; the analog also exhibits native self-assembly. Although affinity for the insulin receptor is decreased ∼20-fold, biological activities in cells and rats were within the range of natural variation. Together, our findings suggest that the invariance of PheB24 among vertebrate insulins and insulin-like growth factors reflects an essential role in enabling efficient protein folding, trafficking, and secretion, a function that is inapparent in native structures. In particular, we envision that the para-hydroxyl group of TyrB24 hinders pairing of cystine B19-A20 in an obligatory on-pathway folding intermediate. The absence of genetic variation at B24 and other conserved sites near this disulfide bridge-excluded due to β-cell dysfunction-suggests that insulin has evolved to the edge of foldability. Nonrobustness of a protein's fitness landscape underlies both a rare monogenic syndrome and "diabesity" as a pandemic disease of civilization.
Knocking out Fkbp51 decreases CCl4-induced liver injury through enhancement of mitochondrial function and Parkin activity
(Springer Nature, 2024-01-02) Qiu, Bin; Zhong, Zhaohui; Dou, Longyu; Xu, Yuxue; Zou, Yi; Weldon, Korri; Wang, Jun; Zhang, Lingling; Liu, Ming; Williams, Kent E.; Spence, John Paul; Bell, Richard L.; Lai, Zhao; Yong, Weidong; Liang, Tiebing; Medicine, School of Medicine
Background and aims: Previously, we found that FK506 binding protein 51 (Fkbp51) knockout (KO) mice resist high fat diet-induced fatty liver and alcohol-induced liver injury. The aim of this research is to identify the mechanism of Fkbp51 in liver injury. Methods: Carbon tetrachloride (CCl4)-induced liver injury was compared between Fkbp51 KO and wild type (WT) mice. Step-wise and in-depth analyses were applied, including liver histology, biochemistry, RNA-Seq, mitochondrial respiration, electron microscopy, and molecular assessments. The selective FKBP51 inhibitor (SAFit2) was tested as a potential treatment to ameliorate liver injury. Results: Fkbp51 knockout mice exhibited protection against liver injury, as evidenced by liver histology, reduced fibrosis-associated markers and lower serum liver enzyme levels. RNA-seq identified differentially expressed genes and involved pathways, such as fibrogenesis, inflammation, mitochondria, and oxidative metabolism pathways and predicted the interaction of FKBP51, Parkin, and HSP90. Cellular studies supported co-localization of Parkin and FKBP51 in the mitochondrial network, and Parkin was shown to be expressed higher in the liver of KO mice at baseline and after liver injury relative to WT. Further functional analysis identified that KO mice exhibited increased ATP production and enhanced mitochondrial respiration. KO mice have increased mitochondrial size, increased autophagy/mitophagy and mitochondrial-derived vesicles (MDV), and reduced reactive oxygen species (ROS) production, which supports enhancement of mitochondrial quality control (MQC). Application of SAFit2, an FKBP51 inhibitor, reduced the effects of CCl4-induced liver injury and was associated with increased Parkin, pAKT, and ATP production. Conclusions: Downregulation of FKBP51 represents a promising therapeutic target for liver disease treatment.
Loss of FKBP5 Affects Neuron Synaptic Plasticity: An Electrophysiology Insight
(Elsevier, 2019-03) Qiu, Bin; Xu, Yuxue; Wang, Jun; Liu, Ming; Dou, Longyu; Deng, Ran; Wang, Chao; Williams, Kent E.; Stewart, Robert B.; Xie, Zhongwen; Ren, Wei; Zhao, Zhenwen; Shou, Weinian; Liang, Tiebing; Yong, Weidong; Medicine, School of Medicine
FKBP5 (FKBP51) is a glucocorticoid receptor (GR) binding protein, which acts as a co-chaperone of heat shock protein 90 (HSP90) and negatively regulates GR. Its association with mental disorders has been identified, but its function in disease development is largely unknown. Long-term potentiation (LTP) is a functional measurement of neuronal connection and communication, and is considered one of the major cellular mechanisms that underlies learning and memory, and is disrupted in many mental diseases. In this study, a reduction in LTP in Fkbp5 knockout (KO) mice was observed when compared to WT mice, which correlated with changes to the glutamatergic and GABAergic signaling pathways. The frequency of mEPSCs was decreased in KO hippocampus, indicating a decrease in excitatory synaptic activity. While no differences were found in levels of glutamate between KO and WT, a reduction was observed in the expression of excitatory glutamate receptors (NMDAR1, NMDAR2B and AMPAR), which initiate and maintain LTP. The expression of the inhibitory neurotransmitter GABA was found to be enhanced in Fkbp5 KO hippocampus. Further investigation suggested that increased expression of GAD65, but not GAD67, accounted for this increase. Additionally, a functional GABAergic alteration was observed in the form of increased mIPSC frequency in the KO hippocampus, indicating an increase in presynaptic GABA release. Our findings uncover a novel role for Fkbp5 in neuronal synaptic plasticity and highlight the value of Fkbp5 KO as a model for studying its role in neurological function and disease development.
Loss of mTORC1 signalling impairs β-cell homeostasis and insulin processing
(Nature Communication Group, 2017-07-12) Blandino-Rosano, Manuel; Barbaresso, Rebecca; Jimenez-Palomares, Margarita; Bozadjieva, Nadejda; Werneck-de-Castro, Joao Pedro; Hatanaka, Masayuki; Mirmira, Raghavendra G.; Sonenberg, Nahum; Liu, Ming; Rüegg, Markus A.; Hall, Michael N.; Bernal-Mizrachi, Ernesto; Pediatrics, School of Medicine
Deregulation of mTOR complex 1 (mTORC1) signalling increases the risk for metabolic diseases, including type 2 diabetes. Here we show that β-cell-specific loss of mTORC1 causes diabetes and β-cell failure due to defects in proliferation, autophagy, apoptosis and insulin secretion by using mice with conditional (βraKO) and inducible (MIP-βraKOf/f) raptor deletion. Through genetic reconstitution of mTORC1 downstream targets, we identify mTORC1/S6K pathway as the mechanism by which mTORC1 regulates β-cell apoptosis, size and autophagy, whereas mTORC1/4E-BP2-eIF4E pathway regulates β-cell proliferation. Restoration of both pathways partially recovers β-cell mass and hyperglycaemia. This study also demonstrates a central role of mTORC1 in controlling insulin processing by regulating cap-dependent translation of carboxypeptidase E in a 4EBP2/eIF4E-dependent manner. Rapamycin treatment decreases CPE expression and insulin secretion in mice and human islets. We suggest an important role of mTORC1 in β-cells and identify downstream pathways driving β-cell mass, function and insulin processing.
“Register-shift” insulin analogs uncover constraints of proteotoxicity in protein evolution
(Elsevier, 2020-03-06) Rege, Nischay K.; Liu, Ming; Dhayalan, Balamurugan; Chen, Yen-Shan; Smith, Nicholas A.; Rahimi, Leili; Sun, Jinhong; Guo, Huan; Yang, Yanwu; Haataja, Leena; Phillips, Nelson F. B.; Whittaker, Jonathan; Smith, Brian J.; Arvan, Peter; Ismail-Beigi, Faramarz; Weiss, Michael A.; Biochemistry and Molecular Biology, School of Medicine
Globular protein sequences encode not only functional structures (the native state) but also protein foldability, i.e. a conformational search that is both efficient and robustly minimizes misfolding. Studies of mutations associated with toxic misfolding have yielded insights into molecular determinants of protein foldability. Of particular interest are residues that are conserved yet dispensable in the native state. Here, we exploited the mutant proinsulin syndrome (a major cause of permanent neonatal-onset diabetes mellitus) to investigate whether toxic misfolding poses an evolutionary constraint. Our experiments focused on an invariant aromatic motif (PheB24-PheB25-TyrB26) with complementary roles in native self-assembly and receptor binding. A novel class of mutations provided evidence that insulin can bind to the insulin receptor (IR) in two different modes, distinguished by a "register shift" in this motif, as visualized by molecular dynamics (MD) simulations. Register-shift variants are active but defective in cellular foldability and exquisitely susceptible to fibrillation in vitro Indeed, expression of the corresponding proinsulin variant induced endoplasmic reticulum stress, a general feature of the mutant proinsulin syndrome. Although not present among vertebrate insulin and insulin-like sequences, a prototypical variant ([GlyB24]insulin) was as potent as WT insulin in a rat model of diabetes. Although in MD simulations the shifted register of receptor engagement is compatible with the structure and allosteric reorganization of the IR-signaling complex, our results suggest that this binding mode is associated with toxic misfolding and so is disallowed in evolution. The implicit threat of proteotoxicity limits sequence variation among vertebrate insulins and insulin-like growth factors.
Role of Proinsulin Self-Association in Mutant INS Gene–Induced Diabetes of Youth
(American Diabetes Association, 2020-05) Sun, Jinhong; Xiong, Yi; Li, Xin; Haataja, Leena; Chen, Wei; Mir, Saiful A.; Lv, Li; Madley, Rachel; Larkin, Dennis; Anjum, Arfah; Dhayalan, Balamurugan; Rege, Nischay; Wickramasinghe, Nalinda P.; Weiss, Michael A.; Itkin-Ansari, Pamela; Kaufman, Randal J.; Ostrov, David A.; Arvan, Peter; Liu, Ming; Biochemistry and Molecular Biology, School of Medicine
Abnormal interactions between misfolded mutant and wild-type (WT) proinsulin (PI) in the endoplasmic reticulum (ER) drive the molecular pathogenesis of mutant INS gene-induced diabetes of youth (MIDY). How these abnormal interactions are initiated remains unknown. Normally, PI-WT dimerizes in the ER. Here, we suggest that the normal PI-PI contact surface, involving the B-chain, contributes to dominant-negative effects of misfolded MIDY mutants. Specifically, we find that PI B-chain tyrosine-16 (Tyr-B16), which is a key residue in normal PI dimerization, helps confer dominant-negative behavior of MIDY mutant PI-C(A7)Y. Substitutions of Tyr-B16 with either Ala, Asp, or Pro in PI-C(A7)Y decrease the abnormal interactions between the MIDY mutant and PI-WT, rescuing PI-WT export, limiting ER stress, and increasing insulin production in β-cells and human islets. This study reveals the first evidence indicating that noncovalent PI-PI contact initiates dominant-negative behavior of misfolded PI, pointing to a novel therapeutic target to enhance PI-WT export and increase insulin production.

Browsing by Author "Liu, Ming"

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