UCR

Center for Plant Cell Biology



Members


Dimitrios MorikisDimitrios Morikis

Professor of Bioengineering

Mailing Address:

Bioengineering
Bourns Hall /A229
University of California
Riverside, CA 92521

Phone: (951) 827-2696
Fax: (951) 827-5696
Email: dmorikis@engr.ucr.edu

Website

Degree(s):

B.S. Aristotle University of Thessaloniki, Greece
M.S. Northeastern University, Boston
Ph.D. Northeastern University, Boston

College/Division Affiliation:

Bourns College of Engineering

Center/Inst Affiliation(s):

Center for Plant Cell Biology
Center for Research in Intelligent Systems (CRIS)

Areas Of Expertise:

Computational Molecular Biology; Biomolecular Structure, Dynamics, Electrostatics, and Interactions; Immunophysics; Rational Peptide, Protein, and Drug Design; Structural Bioinformatics ; NMR Spectroscopy

Research Summary:

We follow a cross-disciplinary theoretical and experimental approach, involving biophysics, structural biology, computational chemistry, structural bioinformatics, and bioengineering. Our goals are: (i) to determine structure-dynamics-interactions-function relations for peptides, proteins, protein fragments, and protein complexes, which address basic biological processes; (ii) to design peptides and small proteins with tailored properties and to determine their structure; (iii) to perform rational design for potential therapeutic agents, and (iv) to design de novo peptides of specific structural propensities. Our work is based on the exploration of the dynamic and electrostatic properties of biomolecules and biomolecular complexes using computational methods. We also use nuclear magnetic resonance methods for peptide and protein structure determination. Proteins are dynamic systems, which interact with their surrounding environment. Proteins participate in a wide range of motions and their dynamics are essential for function. Proteins interact with solvent molecules, other proteins, nucleic acids, ligands, prosthetic groups, carbohydrates, lipids, metals, ions, and small molecules. We use molecular dynamics simulations based on the solution of Newton ’s equation of motion to explore the dynamic properties of peptides, proteins, and protein complexes, such as flexibility, mobility, correlated motions, conformational transitions, and folding. Electrostatics plays a significant role in secondary, tertiary, and quaternary structure formation and stability. Electrostatics also plays a significant role in recognition and binding for the formation of protein complexes and multi-component assemblies. We use computational methods based on the solution of the Poisson-Boltzmann equation to explore the electrostatic properties of peptides, proteins, and protein complexes, such as ionization states, desolvation, Coulombic interactions, proton sharing and transfer, conformational transitions, stability, and association. Knowledge of biomolecular structure is the starting point for computational studies at atomic resolution, involving dynamics, electrostatics, thermodynamics, kinetics, and association, which in turn are essential for basic understanding of the physicochemical properties of underlying function. Structure is also the basis of our design efforts for peptides, proteins, and potential therapeutics. We use high-resolution NMR spectroscopy and restrained molecular dynamics-based simulated annealing methods to determine the structure of peptides and small proteins. We also use structural homology methods to model protein structures based on previously solved homologous structures and deposited at the Protein Data Bank. The aim of our structural bioinformatics efforts is to classify proteins according to the spatial distribution of their electrostatic properties, using a combination of structural homology, electrostatic calculations, and similarity indices.

Related Press Releases:

UCR August 8, 2011: Professor Fights Disease that Destroys Vision

The Press Enterprise August 8, 2011: RIVERSIDE: UCR shares $100,000 grant to study eye disease


Selected Publications:

List of publications from HubMed and List of publications from personal website


More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

Career OpportunitiesUCR Libraries
Campus StatusDirections to UCR

Center Information

Center for Plant Cell Biology
Botany & Plant Sciences Department
2150 Batchelor Hall

Tel: (951) 827-7177
Fax: (951) 827-5155
E-mail: genomics@ucr.edu

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