Bryan W Berger

Bryan W Berger
University of Virginia | UVa · Department of Chemical Engineering

Doctor of Philosophy

About

61
Publications
7,758
Reads
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1,512
Citations
Additional affiliations
January 2010 - October 2015
Lehigh University
Position
  • Professor (Assistant)
January 2010 - November 2015
Lehigh University
Position
  • Professor (Associate)
January 2005 - December 2009
Hospital of the University of Pennsylvania
Position
  • PostDoc Position

Publications

Publications (61)
Article
Per- and polyfluoroalkyl substances (PFAS) are a large group of synthetic fluorinated chemicals with surface active and water-repellent properties. The combination of wide-spread use in numerous consumer and industrial products and extended biological half-lives arising from strong carbon-fluorine bonds has led to significant accumulation of PFAS i...
Article
Full-text available
Polysaccharide lyases (PLs) are a broad class of microbial enzymes that degrade anionic polysaccharides. Equally broad diversity in their polysaccharide substrates has attracted interest in biotechnological applications such as biomass conversion to value-added chemicals and microbial biofilm removal. Unlike other PLs, Smlt1473 present in the clini...
Article
Biofilm formation is often attributed to post-harvest bacteria persistence on fresh produce and food handling surfaces. In this study, a predicted glycosyl hydrolase enzyme was expressed, purified and validated for removal of microbial biofilms from biotic and abiotic surfaces under conditions used for chemical cleaning agents. Crystal violet biofi...
Article
Full-text available
Receptor protein tyrosine phosphatases (RPTPs) play critical regulatory roles in mammalian signal transduction. However, the structural basis for the regulation of their catalytic activity is not fully understood, and RPTPs are generally not therapeutically targetable. This knowledge gap is partially due to the lack of known natural ligands or sele...
Article
Polysaccharide lyases (PLs) are an important class of proteins that are excreted from bacteria to degrade sugars in the extracellular matrix of the host. The PL from S. maltophilia (Smlt1473) was found to have pH-specific degradation of three varying polysaccharides: alginate, celluronic acid, and hyaluronic acid (J. Biol. Chem. 289: p18022-18032)....
Preprint
Full-text available
Receptor protein tyrosine phosphatases (RPTPs) are one of the most important, yet least understood, regulators of cell signaling. Particularly, the mechanisms controlling their enzymatic activity have yet to be fully resolved. In contrast to conventional structure-function relationship for receptor tyrosine kinases (RTKs), the activity of RPTPs has...
Article
Hydrophobins are small highly surface‐active fungal proteins with potential as biosurfactants in a wide array of applications. However, practical implementation of hydrophobins at large scale has been hindered by low recombinant yields. In this study, the effects of increasing hydrophobin gene copy number and overexpressing endoplasmic reticulum re...
Article
Full-text available
Abstract Hydrophobins are highly surface-active proteins that have versatile potential as agents for interface engineering. Due to the large and growing number of unique hydrophobin sequences identified, there is growing potential to engineer variants for particular applications using protein engineering and other approaches. Recent applications an...
Article
Small molecules offer powerful ways to alter protein function. However, most proteins in the human proteome lack small-molecule probes, including the large class of non-catalytic transmembrane receptors, such as death receptors. We hypothesized that small molecules targeting the interfaces between transmembrane domains (TMDs) in receptor complexes...
Article
A growing global population and industrialization have come at the cost of induced climate change and pollution of natural resources, resulting in formation of toxic algal blooms in fresh water sources. In the US alone, these blooms cost an estimated $1.5 billion dollars each year to remediate. Current methods to combat such blooms such as copper s...
Article
Hydrophobins are multifunctional, highly surface active proteins produced in filamentous fungi and can be identified by eight conserved cysteine residues, which form four disulfide bridges. These proteins can be subdivided into two classes based on their hydropathy profiles, solubility, and structures formed upon interfacial assembly. Here, we prob...
Article
Full-text available
Biomineralization is an intriguing route towards the low temperature, aqueous phase, green synthesis of inorganic functional nanomaterials. Herein we describe the biomineralization and optical properties of ZnxCd1−xS and ZnxCd1−xS–ZnS quantum confined nanocrystals that have potential application in optoelectronics. The reported biomineralization pr...
Article
This work demonstrates a bioenabled fully aqueous phase and room temperature route to the synthesis of CuInS2/ZnS core/shell quantum confined nanocrystals conjugated to IgG antibodies and used for fluorescent tagging of THP-1 leukemia cells. This elegant, straightforward and green approach avoids the use of solvents, high temperatures and the neces...
Article
Biomineralization is the process by which biological systems synthesize inorganic materials. Herein, we demonstrate an engineered cystathionine ?-lyase enzyme, smCSE, that is active for the direct aqueous phase biomineralization of CdSe and CdSe-CdS core-shell nanocrystals. The nanocrystals are formed in an otherwise unreactive buffered solution of...
Article
Biomineralization is an intriguing approach to the synthesis of functional inorganic materials for energy applications whereby biological systems are engineered to mineralize inorganic materials and control their structure over multiple length scales under mild reaction conditions. Herein we demonstrate a single enzyme mediated biomineralization ro...
Article
An engineered strain of Stenotrophomonas maltophilia (SMCD1) is capable of the direct extracellular biomineralization of CdS quantum dot nanocrystals from buffered aqueous solution of cadmium acetate and L-cysteine without the addition of a chemically reactive precursor. Nanocrystal synthesis is strongly influenced by both the L-cysteine:cadmium ac...
Article
Plexins are transmembrane proteins that serve as guidance receptors during angiogenesis, lymphangiogenesis, neuronal development, and zebrafish fin regeneration with a putative role in cancer metastasis. Receptor dimerization or clustering, induced through extracellular ligand binding but modulated in part by the plexin transmembrane (TM) and juxta...
Article
div class="title">Morphology and Composition of Biomineralized Ceria and Ceria-Zirconia Nanocrystals - Volume 22 Issue S3 - Li Lu, Christopher Curran, Christopher J. Kiely, Bryan W. Berger, Steven Mcintosh
Article
Fibroblast activation protein (FAP) is a cell-surface serine protease which promotes invasiveness of certain epithelial cancers and is therefore a potential target for cancer drug development and delivery. Unlike dipeptidyl peptidase IV (DPPIV), FAP exhibits prolyl endopeptidase activity and is active as a homodimer with specificity for type I coll...
Article
Nature has evolved several unique biomineralization strategies to direct the synthesis and growth of inorganic materials. These natural systems are complex, involving the interaction of multiple biomolecules to catalyze biomineralization and template growth. Herein we describe the first report to our knowledge of a single enzyme capable of both cat...
Article
Biomineralization utilizes biological systems to synthesize functional inorganic materials for application in diverse fields. In the current work, we enable biomineralization of quantum confined PbS and PbS–CdS core–shell nanocrystals and demonstrate their application in quantum dot sensitized solar cells (QDSSCs). An engineered strain of Stenotrop...
Article
Full-text available
Background: Macroalgae represents a promising source of fermentable carbohydrates for use in the production of energy efficient biofuel. The primary carbohydrate in brown algae is the uronic acid-containing alginate, whereas green algae contains a significant amount of glucuronan. A necessary step in the conversion of these polyuronides to bioetha...
Article
Stenotrophomonas maltophilia is an emerging, multidrug-resistant pathogen of increasing importance for the immunocompromised, including cystic fibrosis patients. Despite its significance as an emerging pathogen, relatively little is known regarding the specific factors and mechanisms that contribute to its pathogenicity. We identify and characteriz...
Article
Full-text available
div class="title">Structural and Optical Characterization of Biosynthesized CdS Quantum Dots - Volume 21 Issue S3 - Zhou Yang, Li Lu, Victoria F. Berard, Christopher J. Kiely, Steven Mcintosh, Bryan W. Berger
Article
Full-text available
Nature provides powerful but as-yet largely unharnessed methods for low-cost, green synthesis of inorganic functional materials such as quantum dots. These materials have diverse applications from medicine to renewable energy. Harnessing nature’s unique ability to achieve cost effective and scalable manufacturing solutions with reduced environmenta...
Article
Neuropilins (NRPs) are transmembrane receptors involved in angiogenesis, lymphangiogenesis, and neuronal development as well as in cancer metastasis. Previous studies suggest that NRPs exist in heteromeric complexes with vascular endothelial growth factors (VEGFs) and VEGF receptors as well as plexins and semaphorins. We determined via site-directe...
Article
Full-text available
Plexins (plxns) are transmembrane (TM) receptors involved in the guidance of vascular, lymphatic vessel, and neuron growth as well as cancer metastasis. Plxn signaling results in cytosolic GTPase-activating protein activity, and previous research implicates dimerization as important for activation of plxn signaling. Purified, soluble plxn extracell...
Article
Full-text available
Unlabelled: The diverse Fusobacterium genus contains species implicated in multiple clinical pathologies, including periodontal disease, preterm birth, and colorectal cancer. The lack of genetic tools for manipulating these organisms leaves us with little understanding of the genes responsible for adherence to and invasion of host cells. Actively...
Article
Full-text available
Intrinsically disordered protein regions are widely distributed in the cytoplasmic domains of many transmembrane receptors. The cytoplasmic domain of a disintegrin and metalloprotease (ADAM)10, a transmembrane metalloprotease mediating ectodomain shedding of diverse membrane proteins, was recently suggested to mediate the homodimerization of ADAM10...
Article
Full-text available
Anionic polysaccharides are of growing interest in the biotechnology industry due to their potential pharmaceutical applications in drug delivery and wound treatment. Chemical composition and polymer length strongly influence the physical and biological properties of the polysaccharide and thus its potential industrial and medical applications. One...
Article
Full-text available
Polysaccharide lyases (PLs) catalyze the depolymerization of anionic polysaccharides via a β-elimination mechanism. PLs also play important roles in microbial pathogenesis, participating in bacterial invasion and toxin spread into the host tissue via degradation of the host extracellular matrix, or in microbial biofilm formation often associated wi...
Article
Understanding the basis of specificity in receptor homo- versus heterodimerization is essential to determining the role receptor plays in signal transduction. Specificity in each of the interfaces formed during signal transduction involves cooperative interactions between receptor extracellular (EX), transmembrane (TM), and cytoplasmic (CYTO) domai...
Article
Obtaining high yields of membrane proteins necessary to perform detailed structural study is difficult due to poor solubility and variability in yields from heterologous expression systems. To address this issue, an E. coli-based membrane protein overexpression system utilizing an engineered bacterial outer membrane protein F (pOmpF) fusion has bee...
Conference Paper
Plexins are large transmembrane receptors known to interact with neuropilin 2 co-receptors and semaphorin ligands to regulate neuronal development. These receptors and ligands have recently been implicated in assisting cancer metastasis. While it is understood that plexin signaling occurs via Ras GTPase-activating proteins (Ras GAPs) and semaphorin...
Conference Paper
Over the past 2 decades, surfactants have grown into a $20 billion annual business, with approximately 60% dedicated to industrial processes, 25% to household products and 15% in specialty applications. Most noteworthy is the emergence of specialty applications in the past 10 years, driven in large part by new areas such as biofuels, food p...
Conference Paper
The cost-efficient and energy- efficient generation of renewable fuels will be one of the most important factors in the future economic prosperity of the United States. Solar energy is one of the most promising routes to develop a new, domestic, source of energy. While current solar cells generate electrical power, we need a chemical route to...
Conference Paper
Stenotrophomonas maltophilia is a ubiquitous, Gram-negative bacteria that is of increasing concern to healthcare professionals due to intrinsic multidrug resistance and prevalence as a cause of infection in immunocompromised patients. Major challenges in preventing S. maltophilia exist, such as its high degree of genetic diversity and ability to ra...
Article
Full-text available
Dimerization is a key regulatory mechanism in activation of transmembrane (TM) receptors during signal transduction. This process involves a coordinated interplay between extracellular (EX), TM, and cytoplasmic (CYTO) regions to form a specific interface required for both ligand binding and intracellular signaling to occur. While several transcript...
Conference Paper
Host protease-antiprotease balance has emerged as a major factor in regulating the extent of inflammatory response by neutrophils, macrophages and endothelial cells to bacterial infections. In response to pro-inflammatory cytokines, activated neutrophils release a series of extracellular proteases, including cathepsins, MMPs and neutrophil elastase...
Article
Full-text available
Interactions between transmembrane (TM) helices play an important role in the regulation of diverse biological functions. For example, the TM helices of integrins are believed to interact heteromerically in the resting state; disruption of this interaction results in integrin activation and cellular adhesion. However, it has been difficult to demon...
Article
Integrins are a ubiquitous family of non-covalently associated alpha/beta transmembrane heterodimers linking extracellular ligands to intracellular signaling pathways [1] [Cell, 2002; 110: 673]. Platelets contain five integrins, three beta1 integrins that mediate platelet adhesion to the matrix proteins collagen, fibronectin and laminin, and the be...
Conference Paper
Integrins are a diverse family of adhesion molecules that mediate cell-cell and cell-matrix interactions. Of these, αIIbβ3 has been most extensively characterized, and provides a model for regulation of integrin function. A central feature of integrin regulation is transmembrane (TM) domain interaction: when integrins are inactive, the TM domains o...
Conference Paper
Transmembrane (TM) helices play essential roles in biological processes such as signal transduction, solute transport and membrane protein folding and stability. In order to examine these processes in greater detail, we developed a computational method, CHAMP (computed anti-helical membrane protein), to design peptides which target the TM domains o...
Conference Paper
My general interests lie in understanding the forces that control protein-protein interactions. My work has focused on developing and applying novel experimental methods to characterize these interactions in areas such as protein crystallization, protein-surfactant interactions, membrane protein folding and engineering specificity of transmembrane...
Article
Integrins are a superfamily of transmembrane (TM) α/β heterodimers that mediate fundamental cellular adhesive functions. Platelet integrins, for example, mediate stable platelet adhesion to collagen and fibronectin and the formation of stable platelet aggregates. Integrins reside on cell surfaces in an equilibrium between inactive and active confor...
Article
Single-span transmembrane (TM) helices have structural and functional roles well beyond serving as mere anchors to tether water-soluble domains in the vicinity of the membrane. They frequently direct the assembly of protein complexes and mediate signal transduction in ways analogous to small modular domains in water-soluble proteins. This review hi...
Article
Full-text available
A variety of methods exist for the design or selection of antibodies and other proteins that recognize the water-soluble regions of proteins; however, companion methods for targeting transmembrane (TM) regions are not available. Here, we describe a method for the computational design of peptides that target TM helices in a sequence-specific manner....
Article
The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-beta-D-glucoside were investigated. Osmotic second virial coefficients (B(22)) were measured by self-interaction chromatography using a wide range of additives and precipitants, including polyethylene glycol (PEG) and heptane-1,2,3-...
Article
Integrin are α/β heterodimers that mediate an array of cell-cell and cell-matrix interactions including platelet adhesion and aggregation. Integrins reside on cell surfaces in an equilibrium between inactive and active conformations that are regulated by transmembrane (TM) domain interactions: when integrins are inactive, the TM domains of their α...
Article
Integrins reside on cell surfaces in an equilibrium between inactive and active conformations. When inactive, the transmembrane (TM) domains of integrin α and β subunits interact, but the domains separate when integrins assume their active conformation. Although this conformational change has not been shown for αvβ3, we hypothesized that a peptide...
Article
The effects of various surfactants on the activity and stability of the human adenosine A3 receptor (A3) were investigated. The receptor was expressed using stably transfected HEK293 cells at a concentration of 44 pmol functional receptor per milligram membrane protein and purified using over 50 different nonionic surfactants. A strong correlation...
Article
The interactions leading to crystallization of the integral membrane protein bacteriorhodopsin solubilized in n-octyl-beta-D-glucoside were investigated. Osmotic second virial coefficients were measured by self-interaction chromatography in the presence of sodium malonate, sodium formate and ammonium sulfate. Attractive protein-detergent complex (P...
Article
The interactions leading to crystallization of calcium- and integrin-binding protein (CIB), a novel Ca2+ binding protein, were characterized in terms of osmotic second virial coefficients, B22, measured by self-interaction chromatography. In particular, the role of additives such as alkanediols or DMSO in improving crystal growth in the presence of...
Article
Full-text available
The osmotic second virial coefficient, B(22), has become the quantity most widely used in developing a rational understanding of protein crystallization. In this work a novel method of measuring B22 using self-interaction chromatography (SIC) is presented that is at least an order of magnitude more efficient than traditional characterization method...
Article
The origin of the low steady-state fluorescence quantum yield of some blue-emitting variants of the green fluorescent protein (GFP) is investigated in single-site mutants in which the tyrosine residue at position 66 has been replaced by phenylalanine or by histidine. Time-resolved fluorescence measurements reveal excited-state lifetimes of 74 ps (Y...
Article
Important progress has been made in recent years toward developing a molecular-level understanding of protein phase behavior in terms of the osmotic second virial coefficient, a thermodynamic parameter that characterizes pairwise protein interactions. Yet there has been little practical application of this knowledge to the field of protein crystall...

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Projects (2)
Project
https://www.sciencedirect.com/science/article/pii/S1369703X18300068
Project
To understand structural basis behind molecular functions.