Biological and Chemical Physics Commons^™

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Revealing The Role Of Electrostatics In Molecular Recognition, Ion Binding And Ph-Dependent Phenomena, Mihiri Hewa Bosthanthirige

All Dissertations

In this dissertation, we study the role of electrostatics in molecular recognition, ion binding and pH-dependent phenomena. In this work that includes three different research projects, the Poisson-Boltzmann (PB) model is used to describe the biological system and Delphi (which is a popular tool for solving the PB equation (PBE)) to study the electrostatics of biomolecular systems.

Chapter two aims to investigate the role of electrostatic forces in molecular recognition. We calculated electrostatic forces between binding partners separated at various distances. To accomplish this goal, we developed a method to find an appropriate direction to move one chain of protein …

Supertertiary Structural Dynamics Modulate Function In Postsynaptic Density Protein 95, George L. Hamilton Iii

All Dissertations

Proteins, RNA, and DNA serve as the primary sub-cellular machinery that give rise to the necessary functions of life. The long-standing paradigm has been that the structures of biomolecules, or the arrangement of the subunits that make up a biomolecule, determine biological function. However, biomolecules are not static objects. Instead, they often undergo structural rearrangements that are crucial to enabling and regulating their functions. In my thesis I present several studies of the interplay between the structures, dynamics, and functions of biomolecules that combine experimental fluorescence spectroscopy and computational methods to probe these systems at the single-molecule level. In particular, …

Optimization Of Modular, Long-Range, Ultra-Fast Optical Tweezers With Fluorescence Capabilities For Single-Molecule And Single-Cell Based Biophysical Measurements, Subash C. Godar

All Dissertations

An Optical tweezer is a tightly focused laser beam that applies and senses precise and localized optical force to a dielectric microsphere and offers a unique and effective tool for manipulating the single cell or cell components, including nucleotides and dynein motor proteins. Here, I used highly stabilized optomechanical components and ultra-sensitive detection modules to significantly improve the measurement capabilities over a wide range of temporal and spatial scales. I combined the optical tweezer-based force spectroscopy technique with fluorescence microscopy to develop an integrated high-resolution force-fluorescence system capable of measuring displacements at sub-nanometer, forces at sub-piconewton over a temporal range …

Prediction Of Pathogenic Mutations In Spermine/Spermidine Synthases, Shannon Bonomi

All Theses

As genetic technology and information become continuously more sophisticated and applied to the prevention and treatment of diseases, the need to understand the effects of genetic variants becomes an important task with regards to assessing disease risk. In the specific case of intellectual disabilities, prenatal screenings is an important diagnostic tool that prepares families and health professionals for the arrival of a child who may need immediate, specialized care. Cell Free DNA screenings are routine for determining sex and provide the opportunity to discover genetic anomalies. However, this has little value unless mutations can be recognized as pathogenic and are …

Development, Validation, And Application Of Analytical Methods For Characterizing Adsorbed Protein Orientation, Conformation, And Bioactivity, Aby Thyparambil

All Dissertations

The structure and bioactivity of adsorbed proteins are tightly interrelated and play a key role in their interaction with the surrounding environment. These factors are of critical importance in many biotechnological applications. However, because the bioactive state of an adsorbed protein is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary …

Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic

All Dissertations

In the last two decades nanotechnology market has undergone remarkable growth. Breakthroughs in nanomaterial synthesis increased diverse nanomaterials production and subsequently their application. Owing to its large surface to volume ratio and remarkable physical properties not seen in the bulk materials, nanoparticles are finding emerging use in industry and medicine. Hence, it is expectable that at some point these nanomaterials will end up released into the environment and interact with bio systems. The purpose of this dissertation is to elicit implications of nanomaterial transformation once it gets inside biological milieu.

Rational Design Of Small-Molecule Stabilizers Of Spermine Synthase Dimer By Virtual Screening And Free Energy-Based Approach, Zhe Zhang, Virginie Martiny, David Lagorce, Yoshihiko Ikeguchi, Emil Alexov, Maria A. Miteva

Publications

Snyder-Robinson Syndrome (SRS) is a rare mental retardation disorder which is caused by the malfunctioning of an enzyme, the spermine synthase (SMS), which functions as a homo-dimer. The malfunctioning of SMS in SRS patients is associated with several identified missense mutations that occur away from the active site. This investigation deals with a particular SRS-causing mutation, the G56S mutation, which was shown computationally and experimentally to destabilize the SMS homo-dimer and thus to abolish SMS enzymatic activity. As a proof-of-concept, we explore the possibility to restore the enzymatic activity of the malfunctioning SMS mutant G56S by stabilizing the dimer through …

Protein Nano-Object Integrator: Generating Atomic-Style Objects For Use In Molecular Biophysics, Nicholas Smith

All Theses

As researchers obtain access to greater and greater amounts of computational power, focus has shifted towards modeling macroscopic objects while still maintaining atomic-level details. The Protein Nano-Object Integrator (ProNOI) presented here has been designed to provide a streamlined solution for creating and designing macro-scale objects with atomic-level details to be used in molecular simulations and tools. To accomplish this, two different interfaces were developed: a Protein Data Bank (PDB), PDB-focused interface for generating regularly-shaped three-dimensional atomic objects and a 2D image-based interface for tracing images with irregularly shaped objects and then extracting three-dimensional models from these images. Each interface is …

Problm Web Server: Protein And Membrane Placement And Orientation Package, Taylor Kimmett, Nicholas Smith, Shawn Witham, Marharyta Petukh, Subhra Sarkar, Emil Alexov

Publications

The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of …

Computational And Experimental Approaches To Reveal The Effects Of Single Nucleotide Polymorphisms With Respect To Disease Diagnostics, Tugba G. Kucukkal, Ye Yang, Susan C. Chapman, Weiguo Cao, Emil Alexov

Publications

DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and …

Chronic Beryllium Disease: Revealing The Role Of Beryllium Ion And Small Peptides Binding To Hla-Dp2, Marharyta Petukh, Bohua Wu, Shannon Stefl, Nick Smith, David Hyde-Volpe, Li Wang, Emil Alexov

Publications

Chronic Beryllium (Be) Disease (CBD) is a granulomatous disorder that predominantly affects the lung. The CBD is caused by Be exposure of individuals carrying the HLA-DP2 protein of the major histocompatibility complex class II (MHCII). While the involvement of Be in the development of CBD is obvious and the binding site and the sequence of Be and peptide binding were recently experimentally revealed [1], the interplay between induced conformational changes and the changes of the peptide binding affinity in presence of Be were not investigated. Here we carry out in silico modeling and predict the Be binding to be within …

On The Modeling Of Polar Component Of Solvation Energy Using Smooth Gaussian-Based Dielectric Function, Lin Li, Chuan Li, Emil Alexov

Publications

Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine …

On The Electrostatic Properties Of Homodimeric Proteins, Brandon Campbell, Marharyta Petukh, Emil Alexov, Chuan Li

Publications

A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily …

A Novel P.Leu(381)Phe Mutation In Presenilin 1 Is Associated With Very Early Onset And Unusually Fast Progressing Dementia As Well As Lysosomal Inclusions Typically Seen In Kufs Disease, Natalia Dolzhanskaya, Michael A. Gonzalez, Fiorella Sperziani, Shannon Stefl, Jeffrey Messing, Guang Y. Wen, Emil Alexov, S Stephan Zuchner, Milen Velinov

Publications

Whole exome sequencing in a family with suspected dominant Kufs disease identified a novel Presenilin 1 mutation p.Leu(381)Phe in three brothers who, along with their father, developed progressive dementia and motor deficits in their early 30s. All affected relatives had unusually rapid disease progression (on average 3.6 years from disease onset to death). In silico analysis of mutation p.Leu(381)Phe predicted more detrimental effects when compared to the common Presenilin 1 mutation p.Glu(280)Ala. Electron microscopy study of peripheral fibroblast cells of the proband showed lysosomal inclusions typical for Kufs disease. However his brain autopsy demonstrated typical changes of Alzheimer disease.

Molecular Mechanisms Of Disease-Causing Missense Mutations, Shannon Stefl, Hafumi Nishi, Marharyta Petukh, Anna R. Panchenko, Emil Alexov

Publications

Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions, and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies which illustrate the association between missense mutations and diseases. In addition we …

Continuous Development Of Schemes For Parallel Computing Of The Electrostatics In Biological Systems: Implementation In Delphi, Chuan Li, Marharyta Petukh, Lin Li, Emil Alexov

Publications

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization …

Cancer Missense Mutations Alter Binding Properties Of Proteins And Their Interaction Networks, Hafumi Nisha, Manoj Tyagi, Shaolei Teng, Benjamin A. Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R. Panchenko

Publications

Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of mutations on protein-protein, protein-nucleic acid and protein-ion binding interfaces. Although some missense mutations over-stabilize protein complexes, we found that the overall effect of mutations is destabilizing, mostly affecting the electrostatic component of binding energy. We also showed that mutations on interfaces resulted in more drastic changes of amino acid physico-chemical …

The Role Of Protonation States In Ligand-Receptor Recognition And Binding, Marharyta Petukh, Shannon Stefl, Emil Alexov

Publications

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa’s and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound …

In Silico Modeling The Effect Of Single Point Mutations And Rescuing The Effect By Small Molecules Binding, Zhe Zhang

All Dissertations

Single-point mutation in genome, for example, single-nucleotide polymorphism (SNP) or rare genetic mutation, is the change of a single nucleotide for another in the genome sequence. Some of them will result in an amino acid substitution in the corresponding protein sequence (missense mutations); others will not. This investigation focuses on genetic mutations resulting in a change in the amino acid sequence of the corresponding protein. This choice is motivated by the fact that missense mutations are frequently found to affect the native function of proteins by altering their structure, interaction and other properties and cause diseases. A particular disease is …

Progress In Developing Poisson-Boltzmann Equation Solvers, Chuan Li, Marharyta Petukh, Emil Alexov

Publications

This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to …

A Rational Free Energy-Based Approach To Understanding And Targeting Disease-Causing Missense Mutations., Zhe Zhang, Shawn Witham, Marharita Petukh, Gautier Moroy, Maria Miteva, Yoshihiko Ikeguchi, Emil Alexov

Publications

BACKGROUND AND SIGNIFICANCE:

Intellectual disability is a condition characterized by significant limitations in cognitive abilities and social/behavioral adaptive skills and is an important reason for pediatric, neurologic, and genetic referrals. Approximately 10% of protein-encoding genes on the X chromosome are implicated in intellectual disability, and the corresponding intellectual disability is termed X-linked ID (XLID). Although few mutations and a small number of families have been identified and XLID is rare, collectively the impact of XLID is significant because patients usually are unable to fully participate in society.

OBJECTIVE:

To reveal the molecular mechanisms of various intellectual disabilities and to suggest …

Enhancing Human Spermine Synthase Activity By Engineered Mutations, Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov

Publications

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an …

Delphi Web Server: A Comprehensive Online Suite For Electrostatic Calculations Of Biological Macromolecules And Their Complexes., Subhra Sarkar, Shawn Witham, Jie Zhang, Maxim Zhenirovskyy, Walter Rocchia

Publications

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output …

Between Algorithm And Model: Different Molecular Surface Definitions For The Poisson-Boltzmann Based Electrostatic Characterization Of Biomolecules In Solution, Sergio Decherchi, José Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov, Walter Rocchia

Publications

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric …

In Silico Investigation Of Ph-Dependence Of Prolactin And Human Growth Hormone Binding To Human Prolactin Receptor, Lin Wang, Shawn Witham, Zhe Zhang, Michael E. Hodsdon, Emil Alexov

Publications

Experimental data shows that the binding of human prolactin (hPRL) to human prolactin receptor (hPRLr-ECD) is strongly pH-dependent, while the binding of the same receptor to human growth hormone (hGH) is pH-independent. Here we carry in silico analysis of the molecular effects causing such a difference and reveal the role of individual amino acids. It is shown that the computational modeling correctly predicts experimentally determined pKa’s of histidine residues in an unbound state in the majority of the cases and the pH-dependence of the binding free energy. Structural analysis carried in conjunction with calculated pH-dependence of the binding revealed that …

Using Delphi Capabilities To Mimic Protein's Conformational Reorganization With Amino Acid Specific Dielectric Constants, Lin Wang, Zhe Zhang, Walter Rocchia, Emil Alexov

Publications

Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to …

Protein Nano-Object Integrator (Pronoi) For Generating Atomic Style Objects For Molecular Modeling, Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li, Emil Alexov

Publications

Background

With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system.

Results

Here we report the Protein Nano-Object Integrator (ProNOI) which allows for …

Highly Efficient And Exact Method For Parallelization Of Grid-Based Algorithms And Its Implementation In Delphi, Chuan Li, Lin Li, Jie Zhang, Emil Alexov

Publications

The Gauss–Seidel (GS) method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the GS method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here, we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of processes or computing units. In …