• MCU is for 3D structure determination facility for macromolecules.
  • The knowledge of accurate molecular structures is a pre-requisite
  • for rational drug design, and for structure-based functional studies
  • to aid the development of effective therapeutic agents and drugs.






Research





Who We Are

Our research interests are in the area of structural biology and biochemistry of importance to a new generation of antimicrobials and bioremediation of plastics and pesticides.My group has done the structural determination of important drug targets from various microbes. The lab is in the quest to develop novel biocatalysts for sustainable processes as well as the build-up novel therapeutics.






Publications





SrNo.
Title
Journal Name Download
1. Structural Insight into the Expanded PCB-Degrading Abilities of a Biphenyl Dioxygenase Obtained by Directed Evolution Journal of Molecular Biology ClickToDownload
2. An insilico approach to structural elucidation of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Arabidopsis thaliana: Hints for herbicide design Phytochemistry ClickToDownload
3. Structural analysis of chorismate synthase from Plasmodium falciparum:A novel target for antimalaria drug discovery International Journal of Biological Macromolecules ClickToDownload
4. Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme Journal Of Biological Chemistry ClickToDownload
5. Retuning Rieske-type Oxygenases to Expand Substrate Range Journal Of Biological Chemistry ClickToDownload

SrNo.
Title
Journal Name Download
1. Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase Biochemical and Biophysical Research Communications ClickToDownload
2. Biochemical, Mutational and In-Silico Structural Evidence for a Functional Dimeric Form of the Ornithine Decarboxylase from Entamoeba histolytica PLOS ONE ClickToDownload
3. Structure-Function Studies of DNA Binding Domain of Response Regulator KdpE Reveals Equal Affinity Interactions at DNA Half-Sites PLOS ONE ClickToDownload
4. Structural basis for dual inhibitory role of tamarind Kunitz inhibitor (TKI) against factor Xa and trypsin The FEBS Journal ClickToDownload
5. Crimean-Congo Hemorrhagic Fever Virus: Strategies to Combat with an Emerging Threat to Human Current Bioinformatics ClickToDownload

SrNo.
Title
Journal Name Download
1. X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications Biochimica et Biophysica Acta ClickToDownload
2. Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5 Proteins: Structure, Function, and Bioinformatics ClickToDownload
3. Crystal Structure of Aura Virus Capsid Protease and Its Complex with Dioxane: New Insights into CapsidGlycoprotein Molecular Contacts PLOS ONE ClickToDownload
4. Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes PLOS ONE ClickToDownload
5. Structural Insight into DFMO Resistant Ornithine Decarboxylase from Entamoebahistolytica : An Inkling to Adaptive Evolution PLOS ONE ClickToDownload
6. Structural Investigation of a Novel N-Acetyl Glucosamine Binding Chi-Lectin Which Reveals Evolutionary Relationship with Class III Chitinase PLOS ONE ClickToDownload

SrNo.
Title
Journal Name Download
1. trans-Protease Activity and Structural Insights into the Active Form of the Alphavirus Capsid Protease Journal of Virology ClickToDownload
2. Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5. Proteins missing

SrNo.
Title
Journal Name Download
1. Crystal structure of a periplasmic solute binding protein in metal-free, intermediate and metal-bound states from Candidatus Liberibacter asiaticus Journal of Structural Biology ClickToDownload
2. Ligand-bound structures of 3-deoxy-D-mannooctulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveal a water channel connecting to the active site for the second step of catalysis Acta Crystallographica Section D ClickToDownload
3. Structural and functional evolution of chitinase-like proteins from plants Proteomics ClickToDownload
4. Kinetic characterization of trans-proteolytic activity of Chikungunya virus capsid protease and development of a FRET-based HTS assay Sci Rep missing

SrNo.
Title
Journal Name Download
1. Inhibition of chikungunya virus by picolinate that targets viral capsid protein Virology ClickToDownload
2. Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition Journal of Structural Biology ClickToDownload
3. Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin Biochemistry ClickToDownload
4. Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D B-Lactamase of Acinetobacter baumannii Antimicrobial Agents and Chemotherapy ClickToDownload
5. Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase Journal of Bacteriology ClickToDownload
6. Characterization of substrate binding and enzymatic removal of a 3-methyladenine lesion from genomic DNA with TAG of MDR A. baumannii. MolBiosyst. ClickToDownload

SrNo.
Title
Journal Name Download
1. Structural, Functional and Evolutionary Aspects of Seed Globulins. Protein Pept Lett Missing
2. Acyl chain preference and inhibitor identification of Moraxella catarrhalis LpxA:Insight through crystal structure and computational studies International Journal of Biological Macromolecules ClickToDownload
3. Evaluation of antiviral activity of piperazine against Chikungunya virus targeting hydrophobic pocket of alphavirus capsid protein Antiviral Research ClickToDownload
4. Biodegradation of phthalic acid esters (PAEs) and in silico structural characterization of mono-2-ethylhexyl phthalate (MEHP)hydrolase on the basis of close structural homolog Journal of Hazardous Materials ClickToDownload
5. Conformer and pharmacophore based identification of peptidomimetic inhibitors of chikungunya virus nsP2 proteas Journal of Biomolecular Structure and Dynamics ClickToDownload
6. Purification and Characterization of 2S Albumin from Seeds of Wrightia tinctoria Exhibiting Antibacterial and DNase Activity Protein & Peptide Letters ClickToDownload
7. A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin Nature Scientific Reports ClickToDownload
8. Structure of Chorismate Mutaselike Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Sit Nature Scientific Reports ClickToDownload

SrNo.
Title
Journal Name Download
1. Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket Virology ClickToDownload
2. In vitro metal catalyzed oxidative stress in DAH7PS: Methionine modification leads to structure destabilization and induce amorphous aggregation International Journal of Biological Macromolecules ClickToDownload
3. Structural Based mimicking of phthalic acid esters(PAEs) and inhibition of hACMSD,an important enzyme of the trypotophan kynurenine metabolism pathway International Journal of Biological Macromolecules ClickToDownload
4. Biophysical and in silico interaction studies of aporphine alkaloids with Malonyl-CoA: ACP transacylase (FabD) from drug resistant Moraxella catarrhalis Biochimie missing
5. Crystal structure of chikungunya virus nsP2 cysteine protease reveals a putative flexible loop blocking its active site International Journal of Biological Macromolecules missing
6. Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies Biochimica et Biophysica Acta (BBA) - General Subjects ClickToDownload





Lab Members





Dr. STUTI GAUR

Post Doc
Speciality Medicinal Chemist
Experience 10 years of Experience
Degrees Ph.D.
Research Small Molecule Synthesis

Pooja Kesari

Research Scholar
Speciality Bio Informatics and X-Ray Crystallography
Experience 5 years of Experience
Degrees M. Tech
Research Structure-function studies

Neetu

Research Scholar
Speciality Molecular Biology Protien Bio-Chemistry & structural Biology
Experience 04 years of Experience
Degrees M.Sc.
Research Development of Noval Antimicrobials

Poonam Dhankhar

Research Scholar
Speciality Molecular Biology Protien Bio-Chemistry & structural Biology
Experience 04 years of Experience
Degrees M.Sc.
Research Development of Noval Bio Catalyst

Vikram Dalal

Research Scholar
Speciality Molecular Biology Protien Bio-Chemistry & structural Biology
Experience 04 years of Experience
Degrees M.Sc.
Research Development of Noval Antimicrobials

Jai Krishna Mahto

Research Scholar
Speciality Molecular Biology Protien Bio-Chemistry & structural Biology
Experience 04 years of Experience
Degrees M.Sc.
Research Development of Noval Bio Catalyst

Monika Sharma

Research Scholar
Speciality Bio Informatics and X-Ray Crystallography
Experience 5 years of Experience
Degrees M. Tech
Research Structure-function studies of Proteins

Vishakha Singh

Research Scholar
Speciality Molecular Biology Protien Bio-Chemistry & structural Biology
Experience 04 years of Experience
Degrees M.Sc.
Research Development of Noval Bio Catalyst





Former Lab Members





Sushmita Bhattacharya

SENIOR DOCTOR AT CLINIX
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 09 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Manali Dutta

SENIOR DOCTOR AT CLINIX
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 09 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials & NanoTechnology

Deepak N Patil

SENIOR DOCTOR AT CLINIX
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 09 years of Experience
Degrees Ph.D.
Research Structure Based Drug Design

Shivendra Pratap Singh

Principal Investigator At RCB,Faridabad
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 05 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Aditya Dev

Post-Doc
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 05 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Pramod Kumar

Post-Doc At UUIC,USA
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 09 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Sonali Dhindwal

Post-Doc At University Of City New York,USA
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 04 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials & Bio Catalyst

Madhusudan Rao Katiki

Research Fellow
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 04 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Vijay Kumar Sharma

Resaerch Fellow
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 04 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Anchal Sharma

Research Fellow
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 04 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

Neha Singh

Post-Doc At RCB,Faridabad
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 04 years of Experience
Degrees Ph.D.
Research Development of Bio Catalyst





Jointly Supervised





Shreela Dey

Research Fellow
Speciality Molecular Biology
Experience 07 years of Experience
Degrees Ph.D.
Research Infectious Diseases

Ms. Anamika Singh

Post-Doc At Israel
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 05 years of Experience
Degrees Ph.D.
Research Development of Anti Microbials

P. Selvakumar

Post-Doc At USA
Speciality Molecular Biology Protien Bio-Chemistry & Structural Biology
Experience 06 years of Experience
Degrees Ph.D.
Research Development of Bio Catalyst

Priya Kapur

Post-Doc,USA
Speciality Molecular Biology
Experience 09 years of Experience
Degrees Ph.D.
Research Animal Bio-Technology





Facilities





Protein X-Ray Crystallography

X-ray crystallography is a powerful technique used for determination of three-dimensional atomic resolution structures of macromolecules like proteins and nucleic acids. X-ray diffracted from single crystalline crystal atoms gives a diffraction pattern. Angles and intensities of diffracted beams used to produce three-dimensional picture of electron density. Further, electron density can be used to determine the mean position of atoms which will give complete three dimensional structure of macromolecule.


IsoThermal Titration Calorimetry

Isothermal titration calorimetry (ITC) is a physical technique used to determine the thermodynamic parameters of receptor-ligand interactions in solution. ITC measures the heat evolved or absorbed (Differential power DP), associated with complex formation at constant temperature. This technology provides Affinity constant (KD), Stoichiometry (n), Enthalpy (H) and Entropy (H), Gibb’s free energy (G) in a single reaction.

Protein Purification System

AKTA purifier is fast performance liquid chromatography system run by a program UNICORN that is often used to analyze or purify mixtures of proteins. Columns used with an FPLC can separate macromolecules based on size, charge distribution (ion exchange), hydrophobicity, reverse-phase or biorecognition (as with affinity chromatography).In FPLC, the columns can be used up to maximum pressure of 3-4 MPa (435-580 psi).

UV/VIS -Spectroscopy

UV-visible spectrometer is usually used to measure the absorbance of ultra violet or visible light by a sample, either at a single wavelength or perform a scan over a range in the spectrum.V-visible spectroscopy is a technique that readily allows one to determine the concentrations of substances and therefore enables oneself to study the rates of reactions, and determine rate equations for reactions, from which a mechanism can be proposed. It can be used in the study of enzyme kinetics, in the quantification of DNA and protein/enzyme activity as well as the thermal denaturation of DNA, etc.

Centrifugation Unit

Centrifugation is a technique which involves the application of centrifugal force to separate particles from a solution according to their size, shape, density, viscosity of the medium and rotor speed. Centrifuge puts an object in rotation around a fixed axis , applying a force perpendicular to the axis of spin (outward) that can be very strong. The centrifuge works using the sedimentation principle, where the centrifugal acceleration causes denser substances and particles to move outward in the radial direction.

Orbital Incubator Shaker

It is mainly used as microbial incubator and shaker for microbial growth. It has an ability to shake while maintaining optimal conditions for incubating microbes. This equipment is very useful since, in order for a cell to grow, it needs oxygen and nutrients that require shaking so that they can be distributed evenly around the culture.






Contact Us





Reach us At

Structural Biology and Protein Engineering Lab,
Department of Biotechnology ,
IIT-Roorkee, Roorkee
Uttarakhand 247667,India.
Kumarfbs@iitr.ac.in
Pravindrak.iitr@gmail.com
+91-1332-285072