ETD at Indian Institute of Science
(529 recursos)
Repository of Theses and Dissertations of Indian Institute of Science, Bangalore, India. The repository has been developed to capture, disseminate and preserve research theses of Indian Institute of Science.
Mostrando recursos 1 - 20 de 30
1.
Energetics Of Protein-Carbohydrate Recognition - Swaminathan, C P
The work embodied in this thesis pertains to an attempt to understand better, the molecular basis of protein-carbohydrate recognition. For this purpose a systematic study was undertaken, not only of the energetics of lectin-sugar interactions, which serve as molecular recognition prototype of protein-carbohydrate interactions, but also of the complex effects of solvent water molecules surrounding both the species in solution state. The systems chosen for investigation include the specific recognition of sugars by lectins from diverse families, leguminosae and moraceae. The following salient aspects of the molecular recognition process constitute the focus of this thesis:
Effect of site specifically modified, deoxy-,...
2.
Computer Modeling and Molecular Dynamics Simulation Of Angiogenins And Its Ligand Bound Complexes - Madhusudhan, M S
Computational structural biology
Even with rapid advances in structure determination methods, there is a long gap to be bridged between the number of proteins that have been sequenced and the number whose three-dimensional structures have been experimentally elucidated. Experimentally protein structures are determined by X-ray crystallography or by nuclear magnetic resonance spectroscopy (NMR). X-ray crystal structures give a time averaged picture but little information on conformational dynamics. Though NMR gives dynamical information, the technique cannot be applied to systems whose molecular weight is large. Only small proteins fall within the ken of NMR experiments. In most cases the three dimensional structure...
3.
Non-repetitive Structures In Proteins : Effects Of Side-chain And Solvent Interactions With The Backbone - Narayanan, Eswar
The work presented in this thesis deals with the analysis of protein crystal structures with an emphasis on the stereochemical aspects of the folded conformation of proteins. The various analyses described have been performed on a data-set of 250 high resolution and non-homologous protein structures derived from the Protein Data Bank. The overall objective of the work has been to analyse conformational features of the non-secondary structural regions in proteins and identify structural motifs present therein. The results can be useful in the three-dimensional modelling of proteins, altering the stability of proteins, design of peptide mimics and in understanding the...
4.
Endotoxin Peptide/Protein Interactions: Thermodynamic And Kinetic Analysis - Thomas, Celestine J
Endotoxin or Lipopolysaccharide (LPS) is the invariant structural component of gram negative bacterial outer membranes and is the chief causative factor of Sepsis or endotoxic shock. Sepsis is a syndrome that has very high mortality rates even in this age of excellent therapeutics and critical patient care. The treatment for sepsis till date remains nonspecific and supportive due to lack of effective anti-endotoxic drugs. Sepsis is initiated when the circulating bacteria shed LPS from their cell envelopes. Shed LPS aggregates are recognized by LPS binding proteins and receptors, which activate the host's immune system. Uncontrolled and excessive stimulation of the...
5.
Interaction Of Chaperone SecB With Protein Substrates: A Biophysical Study - Panse, Vikram G
In the cell, as in in vitro, the final conformation of a protein is determined by it's amino acid sequence (1). Some isolated proteins can be denatured and refolded in vitro in absence of extrinsic factors. However, in order to fold in the cell, the newly synthesized polypeptide chain has to negotiate an environment far more complex than that faced by the unfolded chain in vitro. Cells have evolved proteins called chaperones to assist folding and assembly of polypeptides (2). Thus, the linear sequence of a protein not only contains information that specifies the final three-dimensional functional form, but also...
6.
Garlic (Allium Sativum) Agglutinin I: Specificity, Binding And Folding Mechanism - Bachhawat, Kiran
Lectins are a class of proteins that bind to carbohydrates with a high degree of specificity. They are involved in various cellular processes such as, host - pathogen interactions, targeting of proteins within cells, cell - cell interaction, cellular segregation and development. They serve as important tools for probing the carbohydrate structures in biological systems such as cell membranes and also as model systems for elucidating protein - carbohydrate interactions. Lectins are distributed ubiquitously in nature ranging from microorganisms to the plants and animals.
Plant lectins are a group of proteins that according to a recently updated definition comprise all plant...
7.
Structural Studies On Winged Bean Agglutinins - Manoj, N
Lectins are multivalent carbohydrate binding proteins that specifically recognise diverse sugar structures and mediate a variety of biological processes, such as cell-cell and host-pathogen interactions, serum glycoprotein turnover and innate immune responses. Lectins have received considerable attention in recent years on account of their properties which have led to their wide use in research and biomedical applications. Seeds of leguminous plants are rich sources of lectins, but they are also found in all classes and families of organisms. Legume lectins have similar tertiary structures, but exhibit a large variety of quaternary structures. The carbohydrate binding site in them is made...
8.
Structure Function Studies Of Biologically Important Simple Repetitive DNA Sequences - Pataskar, Shashank S.
The recent explosion of DNA sequence information has provided compelling evidence for the following facts. (1) Simple repetitive sequences-microsatellites and minisatellites occur commonly in the human genome and (2) these repetitive DNA sequences could play an important role in the regulation of various genetic processes including modulation of gene expression. These sequences exhibit extensive polymorphism in both length and the composition between species and between organisms of the same species and even cells of the same organism. The repetitive DNA sequences also exhibit structural polymorphism depending on the sequence composition.
The functional significance of repetitive DNA is a well-established fact. The...
9.
Designed ?-Hairpin, ?-Sheet And Mixed ?-? Structures In Synthetic Peptides - Das, Chittaranjan
Synthetic construction of protein molecules has been widely pursued over the last two decades. A primary goal behind de novo protein design has been to build minimal systems by capturing the essential features of protein structures. Such minimal models can be used to understand underlying principles governing folding, structure, and function of proteins molecules. Several approaches envisioning successful construction of synthetic proteins have been described over the years, some of them being admirably successful (DeGrado et al, 1999; Richardson et al> 1992; Baltzer, 1998). Specific patterning of polar and apolar residues in synthetic sequences has been widely used to achieve...
10.
Mechanism Of Anticancer And Antimalarial Action Of A Modulator Of Heat Shock Proteins - Ramya, T N C
This thesis entitled Mechanism of Anticancer and Antimalarial Action of
a Modulator of Heat Shock Proteins describes the successful elucidation of the
mechanism of anticancer and antimalarial action of 15-Deoxyspergualin (DSG).
DSG, a relatively well known immunosuppressant and antitumor molecule has
been demonstrated to kill the malaria parasite in vitro and in vivo (Midorikawa et
al., 1997; Midorikawa et al., 1998). A highly polar molecule, DSG binds the
carboxy terminal EEVD motif of heat shock proteins, Hsp70 and Hsp90,
enhances the ATPase activity of Hsp70 (Nadler et al., 1992; Nadler et al., 1998),
and modulates several seemingly unrelated cellular processes. DSG has also been
demonstrated to inhibit protein synthesis...
11.
Structural Studies On Enzymes From Salmonella Typhimurium Involved In Propionate Metabolism: Biodegradative Threonine Deaminase, Propionate Kinase And 2-Methylisocitrate Lyase - Simanshu, Dhirendra Kumar
I formally joined Prof. M. R. N. Murthys laboratory at the Molecular Biophysics
Unit, Indian institute of Science, on 1st August 2001. During that time, the interest in the laboratory was mainly focused on structural studies on a number of capsid mutants of two plant viruses, sesbania mosaic virus and physalis mottle virus, to gain an insight into the virus structure and its assembly. Besides these two projects, there were a few other collaborative projects running in the lab at that time such as NIa protease from pepper vein banding virus and diaminopropionate ammonia lyase from Escherichia coli with Prof. H....
12.
Stringent Response In Mycobacteria: Molecular Dissection Of Rel - Jain, Vikas
Adaptation to any undesirable change in the environment dictates the survivability of many microorganisms. Such changes generate a quick and suitable response, which guides the physiology of bacteria. Stringent response is one of the mechanisms that can be called a survival strategy under nutritional starvation in bacteria and was first observed in E. coli upon amino acid starvation, when bacteria demonstrated an immediate downshift in the rRNA and tRNA levels (Stent and Brenner 1961). Mutations that rendered bacteria insensitive to amino acid levels were mapped to an RC gene locus, later termed relA because of the relAxed behavior of the...
13.
Biochemical And Molecular Insights Into ?-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) From Plasmodium Falciparum - Kumar, Shailendra
Malaria, caused by Plasmodium, is one of the most devastating infectious diseases of the world in terms of mortality as well as morbidity (WHO, 2002). The development of resistance in the Plasmodium falciparum against the present antimalarials has made the situation very alarming (Trape et al., 2000). To combat this situation, new antimalarials as well as identification of new drug targets are urgently required. The discovery of the presence of type II fatty acid biosynthesis system in the malarial parasite has offered several promising new targets for this mission.
This thesis describes the successful cloning of fabZ from Plasmodium falciparum, its...
14.
Components Of Fatty Acid Synthesis In Plasmodium Falciparum - Sharma, Shilpi
The disease malaria afflicts more than a billion people and kills almost one
to three million of them every year. Of the four species of Plasmodium affecting man viz., P. falciparum, P. vivax, P. ovale and P. malariae, Plasmodium falciparum is the deadliest as it causes cerebral malaria. The situation has become worse with the continuous emergence of drug resistance in the parasite. Therefore, improving existing drugs and deciphering new pathways for drug development are the need of the hour. The discovery of the type II fatty acid biosynthesis pathway in Plasmodium falciparum (Surolia and Surolia, 2001) has opened up new...
15.
Structural Studies On The Enzymes FabI And FabZ Of Plasmodium Falciparum - Pidugu, Lakshmi Swarna Mukhi
The thesis deals with X-ray crystallographic analysis of two enzymes involved in the fatty
acid biosynthesis pathway, known as Fatty Acid Synthase or FAS, of the malarial parasite, Plasmodium falciparum, in order to understand their functions at the atomic level and to provide structural basis for the rational design of antimalarial compounds. Targeting highly specific and well-characterized biochemical pathways to develop effective therapeutic agents has the advantage of designing new drugs or modifying the existing ones based on the details of the known features of the processes. Knowledge of the three-dimensional structures of the molecules involved in the reactions will enhance...
16.
Folding Studies On Peanut Agglutinin : A Lectin With An Unusual Quaternary Structure - Dev, Sagarika
The thesis entitled “Folding studies on Peanut Agglutinin: A lectin with an unusual quaternary structure” deals with the several aspects of the folding of the tetrameric legume lectin Peanut Agglutinin (PNA). PNA is a well studied legume lectin and several interesting observations regarding its unfolding have been published from our laboratory.
The present thesis is an extension of the same work to enrich our knowledge about the folding behaviour of PNA. The thesis describes both experimental as well as theoretical insight on unfolding of PNA.
Chapter 1 is a general discussion on lectins. Lectins are carbohydrate binding
proteins of non immune...
17.
Structural Investigations Of Sugar-Binding And Multivalency In Peanut Lectin - Natchiar, S Kundhavai
Starting with the structure analysis of ConA in the 70s, the crystal structures of hundreds of different lectins and their carbohydrate complexes have been determined. Lectins, multivalent carbohydrate-binding proteins which specifically bind different sugar structures, have received considerable attention in recent times on account of the realization of the importance of protein−sugar interactions, especially at the cell surface, in biological recognition. They occur in plants, animals, fungi, bacteria and viruses. Plant lectins constitute about 40% of the lectins of known structure. They can be classified into five structural groups, each characterized by a
specific fold. Among them, legume lectins constitute the...
18.
Thermodynamic Characterization Of Wild Type And Mutants Of The E.coli Periplasmic Binding Proteins LBP, LIVBP, MBP And RBP - Prajapati, Ravindra Singh
Native states of globular proteins typically show stabilization in the range of 5 to
15 kcal/mol with respect to their unfolded states. There has been a considerable progress in the area of protein stability and folding in recent years, but increasing protein stability through rationally designed mutations has remained a challenging task. Current ability to
predict protein structure from the amino acid sequence is also limited due to the lack of quantitative understanding of various factors that defines the single lowest energy fold or native state. The most important factors, which are considered primarily responsible for the structure and stability of the...
19.
Intracellular Calcium Dynamics In Dendrites Of Hippocampal Neurons Rendered Epileptic And In Processes Of Astrocytes Following Glutamate Pretreatment - Padmashri, R
The fundamental attribute of neurons is their cellular electrical excitability, which is based on the expression of a plethora of ligand- and voltage-gated membrane channels that give rise to prominent membrane currents and membrane potential variations that represent the biophysical substrate underlying the transfer and integration of information
at the cellular level. Dendrites have both an electrical and a biochemical character, which are closely linked. In contrast, glial cells are non-electrically excitable but nevertheless display a form of excitability that is based on variations of the Ca2+ concentration in the cytosol rather than electrical changes in the membrane. Cytoplasmic Ca2+ serves...
20.
Aromatic Interactions In Peptides : Designed Helices And β-Hairpins - Mahalakshmi, R
Design of complex protein folds requires complete understanding of the stereochemical principles that govern polypeptide chain folding. Extensive studies on design and synthesis of specific secondary structures like β-helices, β -sheets and hairpins have taught us that the unnatural amino acid
aminoisobutyric acid (Aib) can be successfully employed for helix nucleation and tight turns of appropriate stereochemistry are facilitated by the use of DPro-Xxx sequences. Availability of such rigid secondary structure scaffolds therefore permits the design of synthetic peptides that can be used as models for investigation of tertiary interactions, primarily that of aromatic residues.
Chapter 1 summarizes the present knowledge...
1.
