Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2

2019 ◽  
Vol 476 (20) ◽  
pp. 2965-2980
Author(s):  
Lalith K. Chaganti ◽  
Shubhankar Dutta ◽  
Raja Reddy Kuppili ◽  
Mriganka Mandal ◽  
Kakoli Bose
Keyword(s):  
Pdz Domain ◽  
Limited Proteolysis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Multifunctional Protein ◽  
Promising Therapeutic Target ◽  
Wide Range ◽  
Structural Details ◽  
Structural Architecture ◽  
First Time

Abstract HAX-1, a multifunctional protein involved in cell proliferation, calcium homeostasis, and regulation of apoptosis, is a promising therapeutic target. It regulates apoptosis through multiple pathways, understanding of which is limited by the obscurity of its structural details and its intricate interaction with its cellular partners. Therefore, using computational modeling, biochemical, functional enzymology and spectroscopic tools, we predicted the structure of HAX-1 as well as delineated its interaction with one of it pro-apoptotic partner, HtrA2. In this study, three-dimensional structure of HAX-1 was predicted by threading and ab initio tools that were validated using limited proteolysis and fluorescence quenching studies. Our pull-down studies distinctly demonstrate that the interaction of HtrA2 with HAX-1 is directly through its protease domain and not via the conventional PDZ domain. Enzymology studies further depicted that HAX-1 acts as an allosteric activator of HtrA2. This ‘allosteric regulation’ offers promising opportunities for the specific control and functional modulation of a wide range of biological processes associated with HtrA2. Hence, this study for the first time dissects the structural architecture of HAX-1 and elucidates its role in PDZ-independent activation of HtrA2.

scholarly journals Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

2013 ◽  
Vol 288 (23) ◽  
pp. 16460-16475 ◽  
Author(s):  
Linda J. Olson ◽  
Ramiro Orsi ◽  
Solana G. Alculumbre ◽  
Francis C. Peterson ◽  
Ivan D. Stigliano ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Mannose Residue ◽  
Glucosidase Ii ◽  
Mannose 6 Phosphate ◽  
First Time ◽  
Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

Rational humanization of the powerful antithrombotic anti-GPIbα antibody: 6B4

2006 ◽  
Vol 96 (11) ◽  
pp. 671-684 ◽  
Author(s):  
Alexandre Fontayne ◽  
Karen Vanhoorelbeke ◽  
Inge Pareyn ◽  
Isabel Van Rompaey ◽  
Muriel Meiring ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Three Dimensional ◽  
Vector System ◽  
Dimensional Structure ◽  
Fab Fragment ◽  
Variable Regions ◽  
Significant Prolongation ◽  
Von Willebrand ◽  
First Time

SummaryFab-fragments of the monoclonal antibody 6B4, raised against human glycoprotein Ibα (GPIbα), have a powerful antithrombotic effect in baboons by blocking the GPIbα binding site for von Willebrand factor (VWF), without significant prolongation of the skin bleeding time. In order to bring this antibody to the clinic,we here humanized for the first time an anti-human GPIbα by variable-domain resurfacing guided by computer modeling. First, the genes coding for the variable regions of the heavy and light chains of 6B4 were cloned and sequenced. Based on this,a three-dimensional structure of the Fv-fragment was constructed by using homology-based modeling, and with this and comparison with antibodies with known structure,”murine” putative immunogenic residues which are exposed, were changed for “human-like” residues. The humanized Fab-fragment, h6B4-Fab, was constructed in the pKaneo vector system, expressed and purified and showed in vitro an unaltered, even slightly higher binding affinity for its antigen than the murine form as determined by different ELISA set-ups and surface plasmon resonance. Finally, injection of doses of 0.1 to 1.5 mg/kg of h6B4-Fab in baboons showed that both pharmacokinetics and ex-vivo bio-activity of the molecule were to a large extent preserved.In conclusion, the method used here to humanize 6B4 by resurfacing resulted in a fully active derivative, which is now ready for further development.

scholarly journals Structure, function and regulation of pyruvate carboxylase

1999 ◽  
Vol 340 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Sarawut JITRAPAKDEE ◽  
John C. WALLACE
Keyword(s):  
Pyruvate Carboxylase ◽  
Limited Proteolysis ◽  
Three Dimensional ◽  
Point Mutations ◽  
Dimensional Structure ◽  
Molecular Defects ◽  
X Ray Crystallography ◽  
Neurotransmitter Substances ◽  
Translational Mechanisms ◽  
Structural Region

Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145 → Ala, Arg451 → Cys, Ala610 → Thr and Met743 → Thr.

scholarly journals Life Experience and DNA Polymorphisms Influence the Brain Epigenome

2013 ◽  
Vol 40 (5) ◽  
pp. 726-727
Author(s):  
Michael O. Poulter
Keyword(s):  
Life Experience ◽  
Cancer Susceptibility ◽  
Methylation Status ◽  
Three Dimensional ◽  
Covalent Modification ◽  
Dna Polymorphisms ◽  
Dimensional Structure ◽  
Fetal Alcohol ◽  
Wide Range ◽  
Biological Outcomes

Although not strictly fitting the category of translational neuroscience, I believe the implications of this study where it was found that variability in DNA sequence, a single nucleotide polymorphism (SNP), can influence the epigenetic status of DNA and this is influenced by childhood trauma should be of wide interest.Epigenetics is a burgeoning field of study that seeks to understand how alterations in DNA structure influence a wide range of biological outcomes ranging from cancer susceptibility to behaviour. Across this spectrum, two basic kinds of structure are most often examined. The first is covalent modification of DNA by methylation and second is the interaction between DNA binding proteins (histones for example) and DNA. Both influence the three dimensional structure of DNA and therefore gene expression. Importantly these dynamics are thought to be influenced by environmental conditions that may be positive or detrimental. For example, fetal alcohol syndrome has been shown to alter the methylation status of DNA accounting for the facial/cranial abnormalities that are often observed in these patients.

scholarly journals Report on the Real Structure of Benzene Molecules and the Thickness of Graphene

2021 ◽  
Author(s):  
Ning Wang ◽  
Dulun Wang
Keyword(s):  
Molecular Structure ◽  
Layer Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Quantum Mechanical ◽  
Ultraviolet Spectroscopy ◽  
Quantum Mechanical Calculations ◽  
Covalent Bonds ◽  
Wide Range ◽  
Long Time

Abstract The problem of the benzene molecular structure has not been solved for a long time. This research proposes a new concept of covalent bonds based on the existing theory: each electron shared by the nucleus corresponds to a half-valent bond, and a half-valent bond can be formed between interval carbon atoms of the benzene ring. A new theory was established. Quantum mechanical calculations results can quantitatively explain experimental results, such as the hydrogenation heat and ultraviolet spectroscopy of benzene. It has solved more than one hundred years of difficult problems. The design of the new structural forms of benzene molecules shows half-valent bonds with dotted lines, which have a wide range of adaptability, and shows the structural forms and reaction formulas of more than dozens of benzene homologs and derivatives. Under the guidance of the new theory, the stacked three-dimensional structure of benzene was explored. The thickness of the three-layer benzene tube is calculated to be almost equal to the thickness of the graphene. Therefore, it is speculated that graphene may be a three layer structure.

scholarly journals The many faces of amyloid: Protein misfolding: failure or function?

2011 ◽  
Vol 33 (5) ◽  
pp. 6-9
Author(s):  
Elizabeth B. Sawyer ◽  
Sarah Perrett
Keyword(s):  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Three Dimensional ◽  
Epigenetic Inheritance ◽  
Dimensional Structure ◽  
Spongiform Encephalopathy ◽  
Wide Range ◽  
The Many ◽  
And Function

The ability of proteins to recognize, bind and manipulate a wide range of other molecules lies at the heart of virtually every cellular process. In order to achieve this, proteins must fold into a precise three-dimensional structure. A failure to achieve this structure, and the associated loss of protein stability and function, results in diseases such as muscular dystrophy and cystic fibrosis. In addition, the misfolding and aggregation of proteins to form fibrillar species is associated with the progression of amyloid diseases such as Alzheimer's and Huntington's and prion diseases including Creutzfeldt– Jakob disease and bovine spongiform encephalopathy (BSE, or ‘mad cow disease’). In this article, we consider advances in the study of protein folding and misfolding and their relevance to biological function. We also explore the issue of protein ‘misfolding’ to form functional aggregated structures, such as the mode of epigenetic inheritance mediated by fungal prions and the formation of amyloid fibrils with positive biological functions in bacteria.

scholarly journals Dendrimers: A New Race of Pharmaceutical Nanocarriers

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Pooja Mittal ◽  
Anjali Saharan ◽  
Ravinder Verma ◽  
Farag M. A. Altalbawy ◽  
Mohammed A. Alfaidi ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Chemical Properties ◽  
Biologically Active ◽  
Dimensional Structure ◽  
Synthesis Mechanism ◽  
Drug Conjugates ◽  
Wide Range ◽  
New Race ◽  
Physical And Chemical ◽  
And Chemical Properties

Dendrimers are nanosized, symmetrical molecules in which a small atom or group of atoms is surrounded by the symmetric branches known as dendrons. The structure of dendrimers possesses the greatest impact on their physical and chemical properties. They grow outwards from the core-shell which further reacts with monomers having one reactive or two dormant molecules. Dendrimers’ unique characteristics such as hyperbranching, well-defined spherical structure, and high compatibility with the biological systems are responsible for their wide range of applications including medical and biomedical areas. Particularly, the dendrimers’ three-dimensional structure can incorporate a wide variety of drugs to form biologically active drug conjugates. In this review, we focus on the synthesis, mechanism of drug encapsulations in dendrimers, and their wide applications in drug delivery.

scholarly journals Seventeen-Armed Star Polystyrenes in Various Molecular Weights: Structural Details and Chain Characteristics

Polymers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1894
Author(s):  
Jia Chyi Wong ◽  
Li Xiang ◽  
Kuan Hoon Ngoi ◽  
Chin Hua Chia ◽  
Kyeong Sik Jin ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Structural Parameters ◽  
Three Dimensional ◽  
Star Polymers ◽  
Star Polymer ◽  
Dimensional Structure ◽  
Density Profiles ◽  
Molecular Weights ◽  
Radiation Sources ◽  
Structural Details

Star-shaped polymers are very attractive because of their potential application ability in various technological areas due to their unique molecular topology. Thus, information on the molecular structure and chain characteristics of star polymers is essential for gaining insights into their properties and finding better applications. In this study, we report molecular structure details and chain characteristics of 17-armed polystyrenes in various molecular weights: 17-Arm(2k)-PS, 17-Arm(6k)-PS, 17-Arm(10k)-PS, and 17-Arm(20k)-PS. Quantitative X-ray scattering analysis using synchrotron radiation sources was conducted for this series of star polymers in two different solvents (cyclohexane and tetrahydrofuran), providing a comprehensive set of three-dimensional structure parameters, including radial density profiles and chain characteristics. Some of the structural parameters were crosschecked by qualitative scattering analysis and dynamic light scattering. They all were found to have ellipsoidal shapes consisting of a core and a fuzzy shell; such ellipse nature is originated from the dendritic core. In particular, the fraction of the fuzzy shell part enabling to store desired chemicals or agents was confirmed to be exceptionally high in cyclohexane, ranging from 74 to 81%; higher-molecular-weight star polymer gives a larger fraction of the fuzzy shell. The largest fraction (81%) of the fuzzy shell was significantly reduced to 52% in tetrahydrofuran; in contrast, the lowest fraction (19%) of core was increased to 48%. These selective shell contraction and core expansion can be useful as a key mechanism in various applications. Overall, the 17-armed polystyrenes of this study are suitable for applications in various technological fields including smart deliveries of drugs, genes, biomedical imaging agents, and other desired chemicals.

CHARACTERIZING THE SPACE OF INTERATOMIC DISTANCE DISTRIBUTION FUNCTIONS CONSISTENT WITH SOLUTION SCATTERING DATA

2010 ◽  
Vol 08 (02) ◽  
pp. 315-335 ◽  
Author(s):  
PARITOSH A. KAVATHEKAR ◽  
BRUCE A. CRAIG ◽  
ALAN M. FRIEDMAN ◽  
CHRIS BAILEY-KELLOGG ◽  
DEVIN J. BALKCOM
Keyword(s):  
Three Dimensional ◽  
Protein Molecule ◽  
Linear Constraints ◽  
Distribution Functions ◽  
Distance Distribution ◽  
Scattering Data ◽  
Dimensional Structure ◽  
Programming Approach ◽  
X Rays ◽  
Wide Range

Scattering of neutrons and X-rays from molecules in solution offers alternative approaches to the study of a wide range of macromolecular structures in their solution state without crystallization. We study one part of the problem of elucidating three-dimensional structure from solution scattering data, determining the distribution of interatomic distances, P(r), where r is the distance between two atoms in the protein molecule. This problem is known to be ill-conditioned: for a single observed diffraction pattern, there may be many consistent distance distribution functions, and there is a risk of overfitting the observed scattering data. We propose a new approach to avoiding this problem: accepting the validity of multiple alternative P(r) curves rather than seeking a single "best." We place linear constraints to ensure that a computed P(r) is consistent with the experimental data. The constraints enforce smoothness in the P(r) curve, ensure that the P(r) curve is a probability distribution, and allow for experimental error. We use these constraints to precisely describe the space of all consistent P(r) curves as a polytope of histogram values or Fourier coefficients. We develop a linear programming approach to sampling the space of consistent, realistic P(r) curves. On both experimental and simulated scattering data, our approach efficiently generates ensembles of such curves that display substantial diversity.

scholarly journals Diagnosed Three-Dimensional Axisymmetric Structure of the Mulhall Tornado on 3 May 1999

2005 ◽  
Vol 62 (7) ◽  
pp. 2373-2393 ◽  
Author(s):  
Wen-Chau Lee ◽  
Joshua Wurman
Keyword(s):  
Cell Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Necessary Condition ◽  
Maximum Pressure ◽  
Wind Fields ◽  
Tangential Wind ◽  
Axisymmetric Structure ◽  
Perturbation Pressure ◽  
First Time

Abstract On 3 May 1999, an unusually large tornado that caused F4-level damage and killed several people was intercepted by the Doppler on Wheels (DOW) mobile radar near Mulhall, Oklahoma, from a range of 4 to 9 km, resulting in high-resolution volumetric data every 55 s up to 1.5-km altitude over a period of 14 min. For the first time, the evolution and three-dimensional structure of a tornado were deduced using the ground-based velocity track display (GBVTD) technique. After the circulation center was determined, the tangential wind and radial wind were derived from the GBVTD technique at each radius and height. In addition, the axisymmetric vertical velocity, angular momentum, vorticity, and perturbation pressure were deduced from the tangential and radial wind fields. This study focuses on the axisymmetric aspects of this tornado. The primary circulation of the Mulhall tornado consisted of an 84 m s−1 peak axisymmetric tangential wind with the radius of maximum wind (RMW) ranging from 500 to 1000 m. The secondary circulation exhibited a two-cell structure characterized by a central downdraft surrounded by an annular updraft near the RMW. The calculated maximum pressure deficit from a 3-km radius to the tornado center at 50-m altitude was −80 hPa. The maximum vorticity during the first 8 min of observation was located inside the RMW away from the tornado center. This vorticity profile satisfied the necessary condition of barotropic instability. As the tornado weakened afterward, the vorticity monotonically increased toward the center. The computed swirl ratios were between 2 and 6, consistent with the observed multiple vortex radar signatures and the vorticity pattern. Swirl ratios were generally smaller during the weakening phase.

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